Patent Publication Number: US-2015065853-A1

Title: System for magnetic resonance spectroscopy of brain tissue for pattern-based diagnostics

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application claims the benefit of U.S. Provisional Patent Application No. 61/261,170, filed on Nov. 13, 2009. 
    
    
     FIELD 
     This document relates to magnetic resonance spectroscopy (“MRS”), and in particular a system and method for pre-processing MRS data of brain tissue for pattern-based diagnostics. 
     BACKGROUND 
     The diagnosis of brain tissue anomalies is an ongoing challenge in modern medicine. Because of the location of the brain within the skull, and the sensitivity of brain tissue to invasive procedures, the diagnosis of suspected brain disease balances the need for timely and accurate diagnosis with the need to minimize damage to the brain tissue in the course of performing diagnostic procedures. The risk of adverse outcomes related to the diagnostic procedures is significant. For example, in 7,500 brain biopsy procedures conducted from 1979 to 1991, the diagnostic accuracy was 91%. However, the morbidity and mortality rates associated with the invasive biopsy procedure were 3.5% and 0.7%, respectively. 
     In addition, early detection leading to early intervention in a brain anomaly is an important consideration. However, due to the dangers associated with biopsy in a situation of recognized tissue anomaly, early detection is typically achieved using non-invasive procedures such as computed tomography (CT) or magnetic resonance imaging (MRI). However, existing non-invasive diagnostic procedures are relatively ineffective at detecting the early stages of a brain anomaly. Based on non-invasive procedures such as CT or MRI scans alone, practitioners cannot consistently distinguish radiation necrosis or benign lesions from malignant tumors. 
     Magnetic resonance spectroscopy (MRS) with pattern recognition has recently shown potential for the non-invasive diagnosis of brain lesions, for direction of surgical or other therapeutic interventions, and for determining prognosis. Patterns indicative of abnormal tissue appear in brain MRS scans before any abnormality is indicated in the corresponding MRI scans. Therefore, use of reliable MRS-based patterns could enable earlier detection of brain tissue anomalies. Further, if the MRS scans contain sufficiently distinctive and reliable markers, MRS diagnostic procedures could augment or substitute for histological grading, guide surgical intervention at tumor margins and areas of local invasion, and monitor radiation or chemo-therapy progress. Whether these potential advantages are realized depends on the predictive quality of computational models based on MRS scan data that in turn depend on the consistency and inherent informational content of the MRS scans. 
     Previous research on a variety of tissue types indicates that 1.5 Tesla (T) MRS scans contain information useful for diagnostic purposes, particularly biomarkers for AT-acetyl aspartate (NAA), choline (Cho), creatinine (Cr), myo-inositol (MI), lactate, and lipids. For example, using an automated two-category classification model, MRS diagnostic procedures achieved a sensitivity of 80% and specificity of 86% for discriminating breast cancer tissue from scar tissue. However, in brain or other tissues, simple biomarker ratios used for diagnosis such as Cho/Cr cannot adequately distinguish malignant lesions from other features such as progressive multifocal leukoencephalopathy, multiple sclerosis, stroke, and scar tissue. 
     The detection of brain lesions using MRS requires recognizing patterns in MRS scans associated with abnormalities. One method involves the interpretation of MRS scan patterns by an expert practitioner. When an expert interprets MRS spectra for diagnostic purposes, he/she may consider the relative amounts or ratios of two or three biomarkers such as Cho/Cr. Spectrum scans are visually examined, peak biomarkers are identified, and peak heights are scaled manually to determine these ratios. MRS peaks, even if not precisely at the expected chemical shift, may be recognized for the biomarker they represent by the relationship of the biomarker peak to the familiar pattern of peaks in the MRS scan. 
     Diagnostic pattern recognition on the whole MRS spectrum, rather than classification based on a few biomarker ratios, is a recent development. The effective use of multiple biomarkers for diagnosis requires not expert, but automated peak identification and quantification. For example, a multicenter study evaluated automated classification of tumors based on proton MRS patterns using linear discriminant analysis and leave-one-out validation to achieve greater than 90% correct classification of the tissue type in scans from multiple instruments and centers. However, the classification scheme of this study was limited to only three types of tumors. In routine practice, the accurate diagnosis of many different types of tumors as well as normal tissue and other types of non-cancerous anomalies is highly desirable. This goal may be achieved using MRS scans of normal tissue and other types of non-cancerous anomalies in the training and external validation sets of an automated diagnostic pattern recognition method. The accuracy and utility of predictive models strongly depend on at least several factors related to the quality of the MRS scans such as the reproducibility of chemical shifts for each biomarker and the potential for confusion among the spectrum classes modeled. 
     For example, spatial variation in B o , the magnetic field strength of the MRS devices, may result in the misalignment of biomarker chemical shifts. The magnetic field strength varies as a function of target tissue depth. Although the scale of the variations in chemical shift is not so great as to cause misidentification of markers under expert interpretation, the same is not true when automated detection of many different biomarkers is required for computerized pattern recognition. Misidentification of biomarkers between data replicates confounds the MRS-based models and effectively decreases peak resolution by spreading the domain over which each diagnostic feature may appear. For example,  FIG. 1  shows an example of the variation in biomarker chemical shifts among several spectra measured from the same tissue type. 
     The non-uniformity of biomarker peaks represents a significant limitation in use of automated MRS-based pattern recognition. High-magnetic-field medical MRI devices produce MRS scans that have greater biomarker peak resolution and therefore superior ability to distinguish proximate, but diagnostically distinct, spectrum features. For example, using a high-powered 8.5T MRS device to analyze tissue samples from fine needle biopsies, breast tissue anomalies were detected with nearly 100% correct categorization and sensitivity for the extent of breast tissue anomalies. However, the high-powered MRS instruments are not nearly as ubiquitous as 1.5T MRS instruments in the medical community. 
     Another approach to enhancing the quality of MRS data is the preprocessing of the raw MRS data prior to analysis. Data preprocessing is a well-known tool used in research fields that utilize high volumes of data containing both signal and noise, such as mass spectrometry, genomics, proteomics, metabolomics, and structure-activity relationships. Common preprocessing techniques typically include normalization, baseline correction, various kinds of weighting, smoothing, variance or other kinds of scaling, and a priori information weighting. In all computational modeling, such as that used for MRS pattern recognition, there is a concern that preprocessing may obscure the informational content of the raw data; validation of the model and its predictions is important in order to assess the value of preprocessing steps. 
     Previous research has highlighted the beneficial effects of preprocessing MRS data using normalization and digitization on the diagnostic outcome of predictive diagnostic models. However, research to date has overlooked the importance of re-calibrating MRS spectra to account for B o  variations in order to realign the chemical shifts as a critical first step in data preprocessing. A need exists in the art for a preprocessing method that minimizes variation in chemical shifts and enhances the resolution of biomarker shifts relative to random noise. Due to the higher consistency of the preprocessed MRS relative to the raw MRS scans, higher resolution of tissue types including healthy tissue, non-malignant tumors, and different types of tumors could be achieved. Further, the higher fidelity signal even when the MRS signal is relatively weak resulting from preprocessing would make possible the earlier detection of tissue anomalies. In addition, preprocessing of MRS data measured using the more commonly available lower-powered MRS devices would make the enhanced diagnostic methodologies using automated MRS pattern detection more widely available. 
     SUMMARY 
     In an embodiment, a method for preprocessing Magnetic Resonance Spectroscopy (MRS) spectrum data may include the steps of providing a raw MRS spectrum data and scaling the raw MRS spectrum data by using a plurality of weighting constants to generate a preprocessed MRS spectrum data. 
     In another embodiment, a method for preprocessing Magnetic Resonance Spectroscopy (MRS) spectrum data may include the steps of: providing a database including raw MRS spectrum data, defined herein as a frequency-domain spectrum resulting from a Fourier transform of a set of free induction decay (FID) data collected by the MRS instrument for a particular tissue sample. The method may further include normalizing the raw spectrum data to generate normalized MRS spectrum data, scaling the normalized MRS spectrum data by using a plurality of weighting constants to generate a weighted MRS spectrum data, and renormalizing the weighted MRS spectrum data to generate a preprocessed MRS spectrum data. 
     In an embodiment, a method for preprocessing MRS spectrum data includes providing a raw MRS spectrum data, recalibrating the raw MRS spectrum data, and scaling the recalibrated MRS spectrum data by using a plurality of weighting constants to generate a preprocessed MRS spectrum data. 
     In yet another embodiment, a method for preprocessing MRS spectrum data may include the steps of: providing a database having raw MRS spectrum data, normalizing the raw spectrum data to generate normalized MRS spectrum data, scaling the normalized MRS spectrum data by using a plurality of weighting constants to generate a weighted MRS spectrum data, and renormalizing the weighted MRS spectrum data to generate a preprocessed MRS spectrum data. 
     In one embodiment, an MRS preprocessing system for preprocessing raw MRS spectrum data may include one or more processors and a plurality of modules configured to be executed by the one or more processors. The plurality of modules may include a normalization module to normalize the raw MRS spectrum data to generate normalized MRS spectrum data. In addition, a recalibration module shifts each of the nuclear magnetic resonance frequencies representing a particular biomarker to a reference nuclear magnetic resonance frequency representing the particular biomarker to generate a recalibrated MRS spectrum data. A variance-weighting module scales the recalibrated MRS spectrum data by using a plurality of weighting constants to generate a weighted MRS spectrum data. Finally, a renormalization module renormalizes the weighted MRS spectrum data to generate a preprocessed MRS spectrum data. 
     In yet another embodiment, a machine-readable media may be encoded with an MRS preprocessing system to process raw MRS spectrum data. The MRS preprocessing system may include machine readable instructions executable by at least one processor to perform the steps of: receiving raw MRS spectrum data at the MRS preprocessing system executing on at least one processor, normalizing the raw MRS spectrum data to generate normalized MRS spectrum data, scaling the normalized MRS spectrum data by using a plurality of weighting constants to generate a weighted MRS spectrum data, and renormalizing the weighted MRS spectrum data to generate a preprocessed MRS spectrum data. 
     In a further embodiment, a machine-readable media may be encoded with an MRS preprocessing system to process raw MRS spectrum data, the MRS preprocessing system comprising machine readable instructions executable by at least one processor to perform the steps of receiving raw MRS spectrum data at the MRS preprocessing system executing on at least one processor; normalizing the raw MRS spectrum data to generate normalized MRS spectrum data; recalibrating the normalized MRS spectrum data; scaling the recalibrated MRS spectrum data by using a plurality of weighting constants to generate a weighted MRS spectrum data; and renormalizing the weighted MRS spectrum data to generate a preprocessed MRS spectrum data. 
     In one embodiment, a method for detecting tissue abnormalities may include the steps of: providing a database including a raw MRS spectrum data, normalizing the raw spectrum data to generate normalized MRS spectrum data, scaling the normalized MRS spectrum data by using a plurality of weighting constants to generate a weighted MRS spectrum data; and renormalizing the weighted MRS spectrum data to generate a preprocessed MRS spectrum data, whereby the preprocessed MRS spectrum data provides a means for detecting tissue abnormalities for pattern recognition diagnostics of a tissue at an accuracy rate of at least 90%. 
     A method for preprocessing MRS spectrum data may include providing a database having a raw MRS spectrum data. The raw spectrum data includes a summary of the signals produced by a tissue sample at a range of nuclear magnetic resonance frequencies with each of the raw spectrum data including one or more Nuclear Magnetic Resonance (NMR) frequencies and corresponding signals measured from the tissue at each NMR frequency, wherein each NMR frequency is provided in the form of a chemical shift, the chemical shift being the percentage shift in a particular NMR frequency relative to the NMR frequency of a reference chemical. The raw spectrum data is normalized to generate normalized MRS spectrum data, and then the normalized MRS spectrum data is scaled using a plurality of weighting constants to generate a weighted MRS spectrum data. Finally, the weighted MRS spectrum data is renormalized to generate a preprocessed MRS spectrum data with the preprocessed MRS spectrum data having a value range from a minimum value of 0 to a maximum value of 1. 
     In one embodiment, a method for detecting a tissue abnormality may include providing a preprocessed MRS spectrum data of a tissue sample made up of a summary of signals produced by the tissue sample at a range of nuclear magnetic resonance frequencies. In addition the preprocessed MRS spectrum data of the tissue sample may include a raw MRS spectrum data subjected to a preprocessing method including normalization, recalibration, scaling by variance-weighting, and renormalization. The method also may include providing a set of preprocessed comparison MRS spectrum data that may include a plurality of preprocessed comparison MRS spectrum data, where each preprocessed comparison MRS spectrum data of the set may include a summary of signals produced by an abnormal tissue sample having a known abnormality at a range of nuclear magnetic resonance frequencies. Further, each preprocessed comparison MRS spectrum data of the set may include a raw comparison MRS spectrum data subjected to a preprocessing method including normalization, recalibration, scaling by variance-weighting, and renormalization. The method may also include comparing the preprocessed MRS spectrum data of the tissue sample to the set of preprocessed comparison MRS spectrum data using a pattern recognition method and identifying the tissue abnormality as the known abnormality of the preprocessed comparison MRS spectrum data that most closely matches the preprocessed MRS spectrum data of the tissue sample. 
     In another embodiment, a method for detecting a tissue abnormality may include providing a preprocessed MRS spectrum data of a tissue sample made up of a summary of signals produced by the tissue sample at a range of nuclear magnetic resonance frequencies. In addition the preprocessed MRS spectrum data of the tissue sample may include a raw MRS spectrum data subjected to a preprocessing method including normalization, recalibration, scaling by variance-weighting, and renormalization. The method also may include providing a set of preprocessed comparison MRS spectrum data that may include a plurality of preprocessed comparison MRS spectra data, where each preprocessed comparison MRS spectrum data of the set may include a summary of signals produced by an abnormal tissue sample having a known abnormality at a range of nuclear magnetic resonance frequencies. Further, each preprocessed comparison MRS spectrum data of the set may include a raw comparison MRS spectrum data subjected to a preprocessing method including normalization, recalibration, scaling by variance-weighting, and renormalization. The method may further include forming a tissue biomarker signal group that may include at least one of the summary of signals produced by the tissue sample at a particular nuclear magnetic resonance frequency representing a particular biomarker and forming a set of comparison tissue biomarker signal groups, where each comparison tissue biomarker signal group of the set may include at least one of the summary of signals produced by an abnormal tissue sample having a known abnormality at a particular nuclear magnetic resonance frequency representing the same particular biomarker as the particular biomarker of the tissue biomarker signal group. The method may also include comparing the tissue biomarker signal group to the set of comparison tissue biomarker signal groups using a pattern recognition method and identifying the tissue abnormality as the known abnormality of the comparison tissue biomarker signal group most closely matching the tissue biomarker signal group of the tissue sample. 
     Additional objectives, advantages and novel features will be set forth in the description which follows or will become apparent to those skilled in the art upon examination of the drawings and detailed description which follows. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  is a graph of the MRS spectra of 24 oligodendroglioma tissue samples; 
         FIG. 2  is a block diagram illustrating a non-limiting exemplary embodiment of an MRS preprocessing system; 
         FIG. 3  is a block diagram illustrating a non-limiting exemplary embodiment of an MRS preprocessing system; 
         FIG. 4  is a flow chart of the processes of a normalization module in a non-limiting exemplary embodiment of an MRS preprocessing system; 
         FIG. 5  is a flow chart of the processes of a chemical shift recalibration module in a non-limiting exemplary embodiment of an MRS preprocessing system; 
         FIG. 6  is a graph showing an MRS spectrum of astrocytoma tissue overlaid with previously reported biomarker locations; 
         FIG. 7A  is a graph comparing fourteen MRS spectra of astrocytoma tissues prior to preprocessing; 
         FIG. 7B  is a graph comparing fourteen MRS spectra of astrocytoma tissues after chemical shift recalibration; 
         FIG. 8  is a flow chart of the processes of a variance-weighting module in a non-limiting exemplary embodiment of an MRS preprocessing system; 
         FIG. 9  is an exemplary weighting function in a non-limiting exemplary embodiment of an MRS preprocessing system; 
         FIG. 10  is a flow chart of the processes of a renormalization module in a non-limiting exemplary embodiment of an MRS preprocessing system; 
         FIG. 11  is a block diagram of an MRS preprocessing system in a non-limiting exemplary embodiment of an MRS preprocessing system; 
         FIG. 12  is a block diagram of an MRS preprocessing system in a non-limiting exemplary embodiment of an MRS preprocessing system; 
         FIG. 13  is a block diagram of an MRS preprocessing system in a non-limiting exemplary embodiment of an MRS preprocessing system; 
         FIG. 14  is a graph summarizing the results of a principal components analysis of normalized, but otherwise not preprocessed MRS spectra; 
         FIG. 15  is a graph summarizing the results of a principal components analysis of preprocessed MRS spectra; and 
         FIG. 16  is a graph summarizing the results of a principal components analysis of preprocessed MRS spectra that included external validation spectra. 
     
    
    
     Corresponding reference characters indicate corresponding elements among the view of the drawings. The headings used in the figures should not be interpreted to limit the scope of the claims. 
     DETAILED DESCRIPTION 
     A Magnetic Resonance Spectroscopy (MRS) preprocessing system is provided that processes MRS spectrum data that includes an array of chemical shift values and corresponding signal values. The preprocessed MRS spectrum data may be subsequently analyzed using techniques including but not limited to visual inspection by an expert practitioner and automated pattern recognition diagnostic systems. Because the MRS preprocessing system compensates for the confounding effects including but not limited to magnetic field heterogeneity in the MRS device and random noise, a much higher efficacy of automated pattern recognition diagnostic methods may be achieved. The preprocessing methods implemented by the MRS preprocessing system may include a chemical shift recalibration in which the chemical shifts in the MRS spectrum data may be adjusted based on the alignment of selected chemical shifts in the MRS spectrum data to coincide with the previously determined chemical shifts of known biomarkers. Another method that may be optionally implemented by the MRS preprocessing system is a variance-weighting method, in which the signal values at chemical shifts corresponding to frequently observed biomarker peaks may be enhanced relative to the signal values at chemical shifts corresponding to random noise, n which relatively few biomarker peaks are observed. 
     Referring to the drawings, a non-limiting exemplary embodiment of an MRS preprocessing system is illustrated and generally indicated as  100  in  FIGS. 2-13 . MRS spectrum data may include one or more signals paired with a corresponding NMR frequency. The signal may correspond to an amount of energy released by charged particles including but not limited to protons in a tissue sample in response to the absorption of applied electromagnetic pulses. The NMR frequency is defined herein as the resonant frequency of an applied electromagnetic pulse used to generate a signal. The various embodiments of the MRS preprocessing system  100  may provide a means for preprocessing raw MRS spectrum data  101  for the detection of tissue abnormalities using methods including but not limited to pattern recognition diagnostics of tissue. Raw MRS spectrum data  101 , as defined herein, is a summary of the signals produced by a tissue sample at a range of different nuclear magnetic resonance frequencies. Each of the spectra in the raw MRS spectra data  101  may include one or more NMR frequencies and the corresponding signals measured from the sample at each NMR frequency. The NMR frequency may be provided in the form of a chemical shift, defined herein as the percentage shift in NMR frequency relative to the NMR frequency of a reference chemical, expressed in parts per million (ppm). In the context of this application, the terms “chemical shift” and “NMR frequency” may be used interchangeably. Biomarkers contained in the sample typically produce a strong signal at a characteristic chemical shift, thereby may result in an identifiable signal peak at the biomarker&#39;s characteristic chemical shift. 
     The preprocessed MRS spectrum data  103  resulting from the processing of the raw MRS spectrum data  101  by embodiments of the MRS preprocessing system  100  may be used to diagnose tissue abnormalities by detecting patterns in the chemical shifts of the MRS spectrum. The chemical shift patterns may be detected by implementing an automated pattern detection method by the MRS preprocessing system  100 . Because the preprocessed MRS spectrum data  103  may be of a more uniform quality than the raw MRS spectrum data  101 , the diagnosis accuracy resulting from preprocessed MRS data  103  may be significantly enhanced relative to the diagnosis accuracy resulting from unprocessed MRS data  101  in various embodiments. 
     MRS Preprocessing System Overview 
     Referring to  FIG. 2 , a non-limiting exemplary embodiment of the MRS preprocessing system  100  may use a combination of chemical shifts and variance weighting for preprocessing raw MRS spectrum data  101  that may be communicated to the MRS processing system  100  by input system  102  or otherwise stored or present in the MRS preprocessing system  100 . Input system  102  may include one or more devices or systems used to generate or transfer an electronic version of one or more raw MRS spectrum data  101  to the MRS preprocessing system  100 . Once the raw MRS spectrum data  101  is preprocessed by the MRS processing system  100 , the preprocessed spectrum data  103  may be passed to an output system  106  for storage and later analysis using a technique including but not limited to known automated pattern recognition diagnostic systems. Alternately, the preprocessed spectra data  103  may stored at the MRS preprocessing system  100 . The MRS preprocessing system  100  may also generate information to the user interface  108 , including but not limited to the status of the preprocessing process, results, or queries for system input. 
     In one non-limiting embodiment, the MRS preprocessing system  100  may include one or more processors  112  that may be embodied by or in one or more distributed or integrated components or systems. The MRS preprocessing system  100  may include a database  110  on which data may be stored and a computer readable media (CRM)  104  on which one or more algorithms, software, modules, data, computer readable instructions, and/or firmware may be loaded and/or operated and/or which may operate on the one or more processors  112  to implement the systems and methods identified herein. In an embodiment, the database may be a storage system that temporarily and/or permanently stores data and may include volatile and/or nonvolatile memory and/or other types of storage systems or devices. 
     MRS Preprocessing System 
     Referring to  FIG. 3 , a block diagram illustrates the modules of a non-limiting exemplary embodiment of the MRS preprocessing system  100  that may execute on the processor  112  to preprocess the raw MRS spectrum data  101 . The MRS preprocessing system  100  may include modules including but not limited to a normalization module  202  for normalizing raw MRS spectrum data  101 , a chemical shift recalibration module  204  for recalibrating the normalized MRS spectrum data  210 , a variance-weighting module  206  for providing a scaling function and scaling the recalibrated MRS spectrum data  212 , and a renormalization module  208  that may optionally renormalize the weighted spectrum data  214  as shall be discussed in greater detail below. 
     The normalization module  202  may process the raw MRS spectrum data  101  and normalize the raw MRS spectrum data  101  such that the signal values at all chemical shifts of the normalized MRS spectrum data  210  may be normalized to values ranging from a normalized minimum value to a normalized maximum value. The chemical shift recalibration module  204  may then recalibrate the normalized MRS spectrum data  210  by re-aligning the chemical shifts corresponding to two or more selected biomarkers to standardized chemical shift values, and may optionally interpolate all remaining chemical shifts in the normalized MRS spectrum data  210  to fall in an even distribution between the two or more re-aligned chemical shifts. The resulting recalibrated MRS spectrum data  212  may be processed by the variance-weighting module  206 , which may scale the data  212  at each chemical shift up or down according to a predetermined schedule based on the observed variance of the signals in a set of reference MRS spectra analyzed previously. The variance-weighted MRS spectrum data  214  may optionally be further processed by the renormalization module  208 , which may renormalizes the data  214  such that the signal values at all chemical shifts of the renormalized MRS spectrum data  215  range from a normalized minimum value to a normalized maximum value. The renormalized MRS spectrum data  215  may be passed to the output system  106  for analysis by techniques including but not limited to visual inspection by an expert practitioner or automated pattern recognition techniques. 
     Normalization Module 
     Referring to  FIG. 4 , a flow chart illustrates the operation of a non-limiting exemplary embodiment of a normalization module  202 . The normalization module  202  may process raw MRS spectrum data  101 , which may include a summary of at least one signal, a minimum signal value, and a maximum signal value. The normalization module  202  may transform all signal values of the raw spectrum data to values ranging from a normalized minimum value to a normalized maximum value range. One non-limiting example of a normalized minimum value is  0 , and one non-limiting example of a normalized maximum value is  1 . At step  302 , the normalization module  202  may access the raw MRS spectrum data  101 , which may be stored on the input system  102 . In this non-limiting exemplary embodiment, the normalization module  202  may determine a minimum signal value of all the signal values in the spectrum at step  304  and may subtract the minimum signal value from all signal values in the MRS spectrum at step  306  to generate a shifted signal. In this embodiment, the shifted signal values of the MRS spectrum may range between a signal value of  0  at the same chemical shift at which the minimum value was determined in step  304  and a maximum signal value. This maximum signal value may be determined in step  308 , and all shifted signal values may be divided by this maximum signal value at step  310  to produce the normalized MRS spectrum data  210 . 
     Chemical Shift Recalibration Module 
       FIG. 5  is a flow chart illustrating the operation of one non-limiting exemplary embodiment of the chemical shift recalibration module  204 . The chemical shift recalibration module  204  may recalibrate the normalized MRS spectrum data  210  by shifting each of the nuclear magnetic resonance frequencies representing a particular biomarker to a reference nuclear magnetic resonance frequency representing the same particular biomarker. At step  402 , the chemical shift recalibration module  204  may process the normalized MRS spectrum data  210  and corrects the chemical shifts of the data  210  to compensate for magnetic field non-homogeneity in the MRS apparatus (not shown). Referring back to  FIG. 5 , two or more reference signal peaks may be identified in the normalized MRS spectrum data  210  at step  404 . Reference signal peaks, as defined herein, are signal peaks corresponding to known biomarkers. For example,  FIG. 6  shows a non-limiting example of an MRS spectrum on which 97 previously documented biomarker peaks (Martinez-Bisbal et al, 2004) have been overlaid. 
     In one embodiment, the reference signal peaks representing particular biomarkers may be identified by inspection of the raw MRS spectrum data  101  by an expert practitioner. In another embodiment, the reference signal peaks may be identified using an automated identification method. The reference signal peaks may be identified by the presence of a signal peak in close proximity to a previously documented chemical shift of a known biomarker&#39;s signal peak in another embodiment. In still another embodiment, the reference signal peaks may be identified by the presence of the peak at a relative position within a previously documented pattern of signal peaks. 
     The chemical shift location of reference signal peaks in the normalized MRS spectrum data  210  may be compared to the previously documented standard chemical shifts at step  406 , and the chemical shifts of the reference signal peaks in the normalized MRS spectrum data  210  may be moved to coincide with the standard chemical shifts at step  408  to generate the recalibrated MRS spectrum data  212 . In addition, the location of all other chemical shifts in the MRS spectrum may be optionally moved based on a linear interpolation using the newly relocated reference signal peaks identified in step  404 , in order to preserve the relative distance of the other chemical shifts relative to the reference signal peaks at step  410 . 
     As a non-limiting illustrative example,  FIG. 7A  and  FIG. 7B  show an overlay of 13 MRS scans before and after recalibration, respectively. In this example, the recalibration of the MRS scans was performed based on two reference signal peaks identified by inspection of the MRS scans by an expert practitioner. 
     Variance-Weighting Module 
     Referring to  FIG. 8 , a flow chart illustrates the operation of a non-limiting exemplary embodiment of a variance-weighting module  206  that may emphasize consistent signal peaks and depress chemical noise in an MRS spectrum. At step  502 , the variance-weighting module  206  may access a recalibrated MRS spectrum data  212  at step  504 . The variance-weighting module  206  may divide each signal value at each chemical shift in the spectrum by the weighting constant at the corresponding chemical shift from a weighting spectrum to generate the weighted MRS spectrum data  214 . 
     A weighting spectrum, as used herein, is a table of chemical shifts and corresponding weighting constants. Alternatively, the weighting spectrum may be defined as a summary of weighted spectrum signals that includes a maximum weighted signal value. Weighting constants, as defined herein, are numerical constants used to increase or decrease the magnitude of the signal value at a given chemical shift, based on a predetermined criterion, including but not limited to the variation in signal values determined from a set of reference MRS spectrum data at the given chemical shift. 
     In one non-limiting exemplary embodiment, the weighting function is the average relative standard variation determined from two or more sets of reference MRS scans, in which each set of reference scans corresponds to a particular tissue type including but not limited to normal or malignant. The two or more sets of reference MRS scans include but are not limited to raw MRS spectrum data  101 , normalized MRS spectrum data  214 , and recalibrated MRS spectrum data  212 . As a non-limiting illustrative example,  FIG. 9  shows an exemplary weighting spectrum. In this example, the relative standard deviations at each chemical shift were determined for a set of reference recalibrated MRS spectrum data  212 . The relative standard deviation, as used herein, is an expression of the variation in signal values relative to the average value of the signal values for a plurality of MRS spectra data, as expressed by formula (I): 
       Relative Standard Deviation=(Standard Deviation)/(Average)×100   (I)
 
     In addition, in various embodiments, the relative standard deviations may be determined for at least one other reference set of MRS data including but not limited to raw MRS spectrum data  101 , normalized MRS spectrum data  214 , and recalibrated MRS spectrum data  212 . In various embodiments, the relative standard deviations of all reference sets may be averaged, yielding a weighting function, including but not limited to the weighting function shown in  FIG. 9 . 
     The relative standard deviation is a relatively large number for a combination of high variation, as expressed by a large standard deviation, or a relatively low overall value, as expressed by a low average. Random noise, for example, typically has a large variation around a zero value, resulting in a large relative standard deviation. Because variance weighting is implemented by dividing the signal value by the relative standard deviation, the signal value of random noise may be reduced greatly relative to the signal value of large-valued signals having relatively low variation in the reference sets of raw MRS spectra data  101 . 
     The scaling of the MRS spectrum data performed by the variance-weighting module  206  represents a significant advancement over existing techniques such as Fisher weighting, which applies a single weighting factor consisting of the ratio of the variance within a group to the ratio of variance between groups uniformly across the signal values in the spectrum. By contrast, the variance-weighting module  206  may derive weighting factors at each individual chemical shift based on the relative standard deviation, which represents the amount of variance relative to the average value of the data. As a result, the signals most likely to contain useful diagnostic information, i.e. those signals having a high average value and low variance, are scaled up relative to random noise. 
     Renormalization Module 
       FIG. 10  is a flow chart illustrating the operation of a non-limiting exemplary embodiment of a renormalization module  208 . The renormalization module  208  at step  602  may process MRS spectrum data including but not limited to scaled MRS spectrum data  214  and may transform all signal values of the spectrum to range from a normalized minimum value to a normalized maximum value. Because the scaled MRS spectrum data  214  may have been normalized by an embodiment of the normalization module  202 , it may not be necessary to subtract the minimum signal value from all other signal values, since the minimum signal value may be the normalized minimum value. Instead, the maximum signal value of the scaled MRS spectrum may be determined at step  604 , and all values of the MRS spectrum may be divided by this value at step  606 , yielding a final preprocessed MRS spectrum data  103  that may be transferred to the output system  106  for subsequent analysis or storage in various embodiments. 
     System Components 
     MRS preprocessing system  100  may include particular components for providing various functions as discussed above. In particular, the computer readable media  104  may include volatile media, nonvolatile media, removable media, non-removable media, and/or other media or mediums that can be accessed by a general purpose or special purpose computing device. For example, computer readable media  104  may include computer storage media and communication media, including computer readable media. Computer storage media further may include volatile, nonvolatile, removable, and/or non-removable media implemented in a method or technology for storage of information, including but not limited to computer readable instructions, data structures, program modules, and/or other data. Communication media may, for example, embody computer readable instructions, data structures, program modules, algorithms, and/or other data, including as or in a modulated data signal. The communication media may be embodied in a carrier wave or other transport mechanism and may include an information delivery method. The communication media may include wired and/or wireless connections and technologies and may be used to transmit and/or receive wired or wireless communications. Combinations and/or sub-combinations of the systems, components, modules, and methods and processes described herein may be made. 
     The input system  102  may include, for example, a hard disk (not shown) that stores the raw MRS spectrum data  101  input files that are read by the MRS preprocessing system  100 . The input system  102  also may include a storage system that stores electronic data, including but not limited to the raw MRS spectrum data  101  and other electronic data files. The input system  102  also may be one or more processing systems and/or communication systems that transmit and/or receive electronic files and/or other electronic document information or data through wireless and/or wire line communication systems, and/or other data to the MRS preprocessing system  100 . 
     The output system  106  may include a communication system that communicates data with another system or component. The output system  106  may be a storage system that temporarily and/or permanently stores data, including but not limited to input files, intermediate data tables generated by the MRS preprocessing system  100 , output files, and/or other data. The output system  106  also may include a computer, one or more processors, one or more processing systems, or one or more processes that further process data. The output system  106  may otherwise include a monitor or other display device, one or more processors, a computer, a printer, another data output device, volatile and/or nonvolatile memory, other output devices, computer readable media, a user interface  108  for displaying data, and/or a combination of the foregoing. The output system  106  may receive and/or transmit data through a wireless and/or wire line communication system. The output system  106  may be embodied by or in or operate using one or more processors or processing systems, one or more distributed or integrated systems, and/or computer readable media. The output system  106  is optional for some embodiments. 
     Identification of Tissue Abnormalities Using Preprocessed MRS Spectrum Data 
     Preprocessed MRS spectrum data  103  produced by various embodiments of the MRS preprocessing system  100  may be used to identify tissue abnormalities using a variety of methods. As one non-limiting example, an expert practitioner may visually compare the preprocessed MRS spectrum data  103  from the sample tissue to one or more comparison MRS spectrum data from tissues having known abnormalities to determine whether an abnormality is present in the sample tissue. In another non-limiting example, an automated pattern recognition algorithm may be used to automatically compare the preprocessed MRS spectrum data  103  from the sample tissue to one or more comparison MRS spectrum data from tissues having known abnormalities to determine whether an abnormality is present in a tissue. 
     Automated pattern recognition algorithms make use of known statistical modeling techniques including but not limited to principal component and discriminant analysis to match the signal patterns of an unknown tissue to the signal patterns within a model resulting from the analysis of the MRS signal patterns from tissues having a variety of known abnormalities. A non-limiting example of a software package that implements an automated pattern recognition method is RESolve 1.2 (Hi-Res version, Colorado School of Mines). The efficacy of any type of pattern recognition method may depend upon at least several factors including the consistency of the data analyzed. 
     The consistency of the MRS spectra data may depend upon at least several factors including but not limited to variation in the type of MRS instrument used to measure the MRS spectra data, the variation in operating parameters within the same MRS instrument over time, and the variation due to the practices of individual MRS technicians when measuring the MRS spectra data. The various embodiments of the MRS preprocessing system  100  may reduce much of the variation between individual MRS spectra data by performing a standardized set of processes to produce each preprocessed MRS spectrum data  103 , rendering the data in a more standardized form for diagnostic purposes. 
     In one non-limiting exemplary embodiment, automated pattern recognition methods may be used to compare the preprocessed MRS spectrum data  103  from an unknown tissue type to a model derived from a set of entire MRS spectra data from tissues having various known abnormalities. In another embodiment, only a subset of the signals from the preprocessed MRS spectrum data  103  from an unknown tissue type corresponding to known biomarkers may be compared to a model derived from subsets of the signals of MRS spectra corresponding to the same biomarkers in tissues with known abnormalities. In this embodiment, the standardization of the MRS spectrum data made possible by the use of the MRS preprocessing system  100  results in diagnostic efficacies that are comparable to the diagnostic efficacies of pattern recognition methods that compare entire MRS spectra. Because only a discrete subset of the MRS spectra corresponding to the biomarkers are used in this embodiment, this method of identifying an unknown tissue type may be used for MRS spectra data obtained for a variety of spectra resolutions. As a result, this method may be used in a wide variety of laboratory and clinical settings equipped with MRS devices of varying resolution. In addition, because this method is resolution-independent, the standardized MRS spectra data from one or more laboratory or clinical facilities may be shared and/or combined as needed. A non-limiting example of a subset of the signals from the preprocessed MRS spectrum data is provided in Table 2 in the Examples below. 
     The preprocessed MRS spectrum data  103  may be derived from any tissue sample capable of measurement by an MRS device without limit. Non-limiting examples of tissue samples that may analyzed using various embodiments include brain tissue, prostate tissue, breast tissue, liver tissue, lung tissue, ovarian tissue, testicular tissue, bladder tissue, tongue tissue, dermal tissue, epidermal tissue, joint tissue, bone tissue, eye tissue, and kidney tissue. In addition, non-limiting examples of tissue abnormalities that may be identified using various embodiments include malignancy, necrosis, neurotoxicity, delamination, hypertrophy, hypotrophy, inflammation, and rheumatism. 
     In one illustrative non-limiting example, an embodiment of the method for detecting a tissue abnormality may be used to identify whether an unknown brain tissue sample possesses an abnormality including but not limited to necrosis, metastasized carcinoma, metastasized melanoma, demyelination, astrocytoma, oligodendroglioma, meningioma, glioblastoma multiforme, or ganglioglioma. In this example, an automated pattern recognition method may be used to match the MRS spectrum pattern of the unknown tissue sample to the model that relates the pattern of a MRS spectrum to each of the possible tissue abnormalities, as well as to the MRS spectrum pattern of normal brain tissue. 
     In another illustrative non-limiting example, an embodiment of the method for detecting a tissue abnormality may be used to determine the stage of a particular cancerous tissue. In this example, an automated pattern recognition method may be used to match the MRS spectrum pattern of the unknown cancerous tissue sample to the model that relates the pattern of a MRS spectrum to each of the possible cancer stages, as well as to the MRS spectrum pattern of normal non-cancerous tissue. 
     Other non-limiting examples of applications of the MRS preprocessing system  100  are provided in the Examples below. 
     Exemplary Embodiments 
       FIG. 11  is a block diagram showing a second non-limiting exemplary embodiment of the MRS preprocessing system  100 A that preprocesses a normalized MRS spectrum data  210 . In this embodiment, the MRS preprocessing system  100 A includes a chemical shift recalibration module  204  that may recalibrate the normalized MRS spectrum data  210 , a variance-weighting module  206  that may scale the recalibrated MRS spectrum data  212  at each chemical shift up or down according to a predetermined weighting function to generate a variance-weighted MRS spectrum data  214  and a renormalization module  208  that may normalize the variance-weighted MRS spectrum data  214  to produce a preprocessed MRS spectrum  103 . 
       FIG. 12  is a block diagram showing a third non-limiting exemplary embodiment of the MRS preprocessing system  100 B that preprocesses raw MRS spectrum data  101 . In this embodiment, the MRS preprocessing system  100 B may include a normalization module  202  to normalize the raw MRS spectrum data  101 , a variance-weighting module  208 A that may scale the recalibrated MRS spectrum data  212  at each chemical shift of the normalized MRS spectrum data  210 , and a renormalization module  208  to normalize the variance-weighted MRS spectrum data  214 , resulting in a preprocessed MRS spectrum data  103 . This particular embodiment does not include a chemical shift calibration module  204 , which simplifies the implementation of the MRS preprocessing system  100 A at the cost of somewhat lower diagnostic efficacy, as presented in the examples below. This embodiment may be suitable for an initial diagnostic procedure for patients with unidentified abnormalities on traditional MR imaging. Once a possible disease state is identified using this simplified embodiment, the raw MRS spectrum data  101  could be preprocessed using an embodiment that includes a chemical shift recalibration module  204  and analyzed using a more accurate predictive diagnostic model. 
       FIG. 13  is a block diagram showing a fourth non-limiting exemplary embodiment of the MRS preprocessing system  100 C that preprocesses a normalized MRS spectrum data  210 . In this embodiment, the MRS preprocessing system  100 B may include a variance-weighting module  206 A that processes the normalized MRS spectrum data  210  and may scale the normalized MRS spectrum data  210  using the variance-based weighting function previously discussed above. The resulting scaled MRS spectrum data  214  may be normalized by the renormalization module  208  to generate a preprocessed MRS spectrum data  103 , which may be optionally transferred to the output system  106  for storage or subsequent analysis. 
     Other non-limiting exemplary embodiments may exclude the normalization module  202  and/or the renormalization module  208 . Yet other non-limiting exemplary embodiments may perform the operations of any combination of embodiments of the normalization module  202 , chemical shift recalibration module  204 , variance-weighting module  206 A, renormalization module  208  or any subset thereof in any order. 
     Diagnostic Applications 
     The preprocessing of MRS spectra as described herein results in MRS spectra of sufficient quality to develop diagnostic models to identify a wide variety of different tissue types. Although the chemical shift peaks corresponding to particular biomarkers used in the preprocessing method may vary depending upon the particular tissue to be diagnosed, the preprocessing methodology is generally applicable. Non-limiting examples of diagnostic models that may be developed using the preprocessed MRS spectra data are summarized in Table 1: 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Application of Diagnostic Models 
               
               
                 Using Pre-processed MRS Spectra 
               
            
           
           
               
               
            
               
                 Diagnostic Application 
                 Diagnostic Value 
               
               
                   
               
               
                 Identify glioblastoma multiforme 
                 Establish need for follow-up 
               
               
                 vs. necrotic tissue 
                 therapy 
               
               
                 Discriminate astrocytoma tissue 
                 Intervention vs. watchful waiting 
               
               
                 grades 2/3/4 
               
               
                 Identify deep brain (basal ganglia 
                 Improved diagnostic efficacy; 
               
               
                 and brainstem) anomalies 
                 biopsy-based yield is non- 
               
               
                   
                 diagnostic 
               
               
                 Diagnosis of metastatic tumor 
                 Origin of primary tumor unknown 
               
               
                 Monitor brain trauma tissue 
                 Need early correlation to eventual 
               
               
                   
                 clinical outcome (return to 
               
               
                   
                 activity, symptom duration) 
               
               
                 WHO CNS Tumor Classification 
                 Improved definition of prognosis 
               
               
                 System 
               
               
                 Lymphoma differential diagnosis 
                 Define treatment options; 
               
               
                 (lymphoma vs. glial neoplasm) 
                 non-surgical intervention is better 
               
               
                   
                 for lymphomas 
               
               
                 Identify tumor tissue 
                 Early diagnosis; define treatment 
               
               
                   
                 options 
               
               
                 Identify tumor tissue type - 
                 Define treatment options 
               
               
                 glioblastoma multiforme, 
               
               
                 metastasis, or abscess 
               
               
                 Differential diagnosis of 
                 Define treatment options 
               
               
                 oligodendroglioma tissue grades 
               
               
                 Differentiate early Alzheimer&#39;s 
                 difficult at early stages; defines 
               
               
                 disease vs. mild cognitive 
                 treatment options 
               
               
                 impairment vs. vascular dementia 
               
               
                 Parkinson&#39;s disease vs. secondary 
                 Early diagnosis; defines treatment 
               
               
                 Parkinson&#39;s disease vs. multiple 
                 options 
               
               
                 system atrophy vs. corticobasil 
               
               
                 degeneration 
               
               
                 Huntingdon&#39;s Disease diagnosis 
                 Early diagnosis; defines treatment 
               
               
                   
                 options 
               
               
                 Human Prion Disease diagnosis 
                 Early diagnosis; defines treatment 
               
               
                 (Creutzfeldt-Jakob disease, 
                 options 
               
               
                 Gerstmann-Sträussler- 
               
               
                 Scheinker syndrome, fatal familial 
               
               
                 insomnia, variant Creutzfeldt-Jakob 
               
               
                 disease, iatrogenic Creutzfeldt-Jakob 
               
               
                 disease, kuru) 
               
               
                 Amyotrophic lateral sclerosis 
                 Early diagnosis and staging; 
               
               
                 diagnosis 
                 defines treatment options 
               
               
                 Repeated Brain Injury 
                 predict recovery or long term 
               
               
                   
                 cognitive defect 
               
               
                 Breast Cancer vs. benign tissues 
                 Determine temporal window for re- 
               
               
                   
                 injury; predict responder vs. non- 
               
               
                   
                 responder; predict metastasis to 
               
               
                   
                 lymph nodes 
               
               
                 Diagnosis of other cancers (ovarian, 
                 Early diagnosis; defines treatment 
               
               
                 prostate, bone, lung, pancreatic, 
                 options 
               
               
                 colon) 
               
               
                 Diagnose arthritis and other joint 
                 Early diagnosis; defines treatment 
               
               
                 diseases 
                 options 
               
               
                 Diagnose any disease state using 
                 Early diagnosis; defines treatment 
               
               
                 measured changes in composition or 
                 options 
               
               
                 concentrations of biological 
               
               
                 components within any tissue; gout, 
               
               
                 arterial plaque, nephritis, high 
               
               
                 blood sugar, and many others 
               
               
                   
               
            
           
         
       
     
     EXAMPLES 
     The following examples illustrate various aspects of the embodiments. 
     Example 1 
     Qualitative Effects of Chemical Shift Recalibration on MRS Spectra 
     To assess the qualitative effects of various preprocessing techniques on the quality of MRS spectra data from various tissue types, the following experiment was conducted. 
     Multiple MRS brain scans associated with nine common brain disease categories and representative normal brain tissue were obtained with institutional approval (UAMS Human Research Advisory Committee, University of Arkansas Medical Sciences Assurance M-1451, IORG0000345). The number of MRS scans obtained in each sample class are summarized in Table 2: 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 MRS Scans Used in Preprocessing Assessment Studies 
               
            
           
           
               
               
               
            
               
                   
                 Scans 
                   
               
            
           
           
               
               
               
               
            
               
                   
                 Used for 
                 Used for 
                   
               
               
                   
                 Model 
                 External 
               
               
                 Sample Class 
                 Training 
                 Validation 
                 Total 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 Normal (N) 
                 20 
                 41 
                 61 
               
               
                 Necrosis (X) 
                 2 
                 0 
                 2 
               
               
                 Metastasized Carcinoma (C) 
                 6 
                 0 
                 6 
               
               
                 Metastasized Melanoma (Z) 
                 2 
                 0 
                 2 
               
               
                 Demyelination (D) 
                 3 
                 0 
                 3 
               
               
                 Astrocvtoma (A) 
                 14 
                 0 
                 14 
               
               
                 Oligodendroglioma (0) 
                 20 
                 4 
                 24 
               
               
                 Meningioma (M) 
                 3 
                 0 
                 3 
               
               
                 Glioblastoma multiforme (G) 
                 20 
                 2 
                 22 
               
               
                 Ganglioglioma (Z) 
                 2 
                 0 
                 2 
               
               
                   
               
            
           
         
       
     
     All MRS spectra data were collected at the University of Arkansas for Medical Sciences (UAMS) using three GE Signa 1.5 Tesla MRIs (Echospeed clinical model LX, GE Medical Systems, Waukesha, Minn., USA) and GE&#39;s double spin echo sequence (PROBE-P). Data were acquired using repetition times of either 1400,1500, or 2000 ms and echo times (TEs) of 35 or 144 ms. All scans were acquired as an extension of the clinical imaging services performed for these patients or from healthy volunteers. 
     With the exception of contralateral brain scans, the identities of training set scans were confirmed by biopsy. Contralateral scans were assumed to be normal based on the absence of any MRI-detectable anomaly. 
     The TE 35 ms data included signals from molecules with fairly short T2 times, including lipids, myo-inositol (MI), glutamine, glutamate, and other amino acids from N-acetyl aspartate (NAA), creatine (Cr), and choline (Cho). In addition, because the TE 35 ms data are also susceptible to water suppression artifacts, these scans may also have contained signals from macromolecules. By contrast, the TE 144 ms data contained only signals from NAA, Cr, Cho, and in some cases lactate (Lac). 
     All data were processed using GE SA/GE software with zero-filling to 4096 points, 2 Hz exponential line broadening, and automatic phasing using the water peak (Webb et al., 1994). Uncorrected MRS spectra data were saved as ASCII files in (ppm, signal intensity) pairs using a proprietary modification to the SA/GE software. A pathological diagnosis was appended to each MRS spectrum file. Spectral samples were blind-coded to protect patient identity and sent to the National Center for Toxicological Research for analysis. 
     For the chemical shift re-calibration, 97 potential chemical shift locations associated with biomarkers from high-grade glioma biopsies (Martinez-Bisbal et al, 2004) were considered. The 97 potential chemical shift locations are shown superimposed on a typical MRS scan of astrocytoma tissue in  FIG. 6 , and the individual biomarkers considered for this experiment are summarized in Table 3: 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Chemical Shifts of Potential Brain Anomaly Biomarkers 
               
            
           
           
               
               
            
               
                 Chemical Shift 
                   
               
               
                 (ppm) 
                 Biomarker 
               
               
                   
               
            
           
           
               
               
            
               
                 0.90 
                 Fatty acids 
               
               
                 0.94 
                 Isoleucine 
               
               
                 0.95 
                 Leucine 
               
               
                 0.96 
                 Leucine 
               
               
                 0.98 
                 Valine 
               
               
                 1.00 
                 Isoleucine 
               
               
                 1.04 
                 Valine 
               
               
                 1.25 
                 Isoleucine 
               
               
                 1.09 
                 Fatty acids 
               
               
                 1.30 
                 Fatty acids 
               
               
                 1.33 
                 Lactate, Threonine 
               
               
                 1.36 
                 Fatty acids 
               
               
                 1.46 
                 Isoleucine, Lysine 
               
               
                 1.47 
                 Alanine 
               
               
                 1.59 
                 Fatty acids 
               
               
                 1.67 
                 Arginine 
               
               
                 1.69 
                 Lysine 
               
               
                 1.71 
                 Leucine 
               
               
                 1.72 
                 Arginine 
               
               
                 1.90 
                 γ-Aminobutunic acid, Lysine 
               
               
                 1.91 
                 Acetate 
               
               
                 1.97 
                 Isoleucine 
               
               
                 2.00 
                 Proline 
               
               
                 2.03 
                 N-acetyl aspartate 
               
               
                 2.04 
                 Glutamate 
               
               
                 2.03 
                 Fatty acids 
               
               
                 2.06 
                 Proline 
               
               
                 2.11 
                 Glutamate 
               
               
                 2.12 
                 Methionine 
               
               
                 214 
                 Glutamine 
               
               
                 2.19 
                 Methionine 
               
               
                 2.25 
                 Fatty acids 
               
               
                 2.27 
                 γ-aminobutyric acid 
               
               
                 2.28 
                 Valine 
               
               
                 2.34 
                 Glutamate 
               
               
                 2.36 
                 Proline 
               
               
                 2.39 
                 Succinate, Malate 
               
               
                 2.44 
                 Glutamine 
               
               
                 2.49 
                 N-acetyl aspartate 
               
               
                 2.63 
                 Methionine 
               
               
                 2.65 
                 Aspartic acid 
               
               
                 2.68 
                 N-acetyl aspartate, Malate 
               
               
                 2.80 
                 Aspartic acid 
               
               
                 2.82 
                 Fatty Acids 
               
               
                 2.86 
                 Asparagine 
               
               
                 2.96 
                 Asparagine 
               
               
                 3.01 
                 γ-Aminobuturic acid, Lysine 
               
               
                 3.03 
                 Creatine 
               
               
                 3.05 
                 Lysine 
               
               
                 3.06 
                 Tyrosine 
               
               
                 3.12 
                 Ethanolamine, Phenylalanine 
               
               
                 319 
                 Cholina, Tyrosina 
               
               
                 3.20 
                 Phosphocholine 
               
               
                 3.22 
                 Arginine 
               
               
                 3.23 
                 Glycerophosphocholine 
               
               
                 3.24 
                 MI 
               
               
                 3.26 
                 Taurine 
               
               
                 3.30 
                 Phenylalanine 
               
               
                 3.34 
                 Proline 
               
               
                 3.40 
                 α-Glucose 
               
               
                 3.42 
                 β-Glucose, Taurine, Proline 
               
               
                 3.46 
                 β-Glucose 
               
               
                 3.49 
                 β-Glucose 
               
               
                 3.52 
                 Choline 
               
               
                 3.53 
                 mI 
               
               
                 3.55 
                 Glycine 
               
               
                 3.56 
                 Glycerol 
               
               
                 3.57 
                 Phosphocholine 
               
               
                 3.58 
                 Threonine 
               
               
                 3.61 
                 Valine, ml 
               
               
                 3.64 
                 Glycerol 
               
               
                 3.67 
                 Glycerophosphocholine, isoleucine 
               
               
                 3.69 
                 α-Glucose 
               
               
                 3.72 
                 β-Glucose 
               
               
                 3.74 
                 Leucine 
               
               
                 3.75 
                 Glutamate 
               
               
                 3.76 
                 Glutamine 
               
               
                 3.77 
                 Lysine, Alanine 
               
               
                 3.78 
                 α-Glucose 
               
               
                 3.79 
                 Ethanolamine, Glycerol 
               
               
                 3.83 
                 α-Glucose, Serine 
               
               
                 3.85 
                 Methionine 
               
               
                 3.87 
                 Arginine 
               
               
                 3.89 
                 Aspartic Acid 
               
               
                 3.90 
                 β-Glucose 
               
               
                 3.93 
                 Creatine, Tyrosine 
               
               
                 3.94 
                 Serine 
               
               
                 3.97 
                 Serine 
               
               
                 3.99 
                 Asparagine 
               
               
                 4.00 
                 Phenylalanine 
               
               
                 4.05 
                 MI 
               
               
                 4.06 
                 Choline 
               
               
                 4.11 
                 Lactate 
               
               
                 4.12 
                 Proline 
               
               
                 4.18 
                 Phosphocholine 
               
               
                 4.25 
                 Threonine 
               
               
                 4.28 
                 Glycerophosphocholine 
               
               
                   
               
            
           
         
       
     
     For re-calibration, two manually identified reference proton MRS peaks were chosen based on the criteria that the MRS peaks were strongly expressed and far apart from one another within a spectrum. Appropriate references biomarker peaks varied on a case-by-case basis. Besides proximity to an expected location, the identity of a useful reference peak was sometimes inferred from its part in a pattern of adjacent peaks from unrelated molecules. This selection strategy was used successfully within groups of MRS spectra from the same lesion class. Identification of reference peaks was also inferred in some cases by the location and intensity of strong peaks resulting from other protons in the same biomarker molecule. 
     Using the chosen reference peaks and custom-designed recalibration/binning software to facilitate operations, each MRS spectrum was translated and re-calibrated. The software moved the selected reference peaks from their observed chemical shifts to their respective reference locations. The software also linearly interpolated all other data points in the MRS spectrum to new positions to generate the re-calibrated spectrum data. 
     A consistent trend in the reference peak assignments relative to the location of the corresponding peak in a spectrum was observed. At both ends of the MRS spectrum the necessary peak location shift was in the same direction and almost the same distance but the re-calibration shift required in the low ppm domain was slightly less than the shift at the high ppm end. The gross similarity in the magnitude of the required shift supported the hypothesis that the need for re-calibration arose from a phenomenon including but not limited to magnetic field strength variation as a function of tumor depth, a phenomenon that had a parallel effect on all protons within a voxel. The difference in relative correction scale with chemical shift highlighted the necessity of at least a two-point recalibration with interpolation to recalibrate the MRS spectrum. 
     The effectiveness of re-calibration is depicted qualitatively in  FIGS. 7A and 7B , which shows a selected region of raw astrocytoma scans prior to and after recalibration respectively. 
     Example 2 
     Qualitative Effects of Variance Weighting on MRS Spectra 
     To assess the qualitative effects of variance weighting techniques on the quality of MRS spectra from various tissue types, the following experiment was conducted. 
     The MRS scan data sets described in Example  1  were preprocessed using a weighting scheme based on spectra consistency. The spectra intensities from the MRS scans were weighted to reduce random variation (noise) relative to the signal peaks from biomarkers that consistently appeared in the scans. One goal of the weighting was to increase the peak resolution and available information content of MRS without biasing tissue classification results. 
     To determine the weighting function, recalibrated spectra determined using the methods of Example 1 were used to ensure that biomarker peaks would occur at consistent locations on the chemical shift axis of each spectrum. In each tissue class, the relative standard deviation (RSD) was calculated for each chemical shift data point using the signal values from all spectra within each tissue class. This process yielded an RSD variance spectrum across the chemical shift domain for each class. 
     The average of all RSD variance spectra from all classes at each chemical shift was then determined, resulting in a single spectrum of weighting factors. This weighting function, when divided into an MRS spectrum, would not bias the determination of tissue class identity using pattern recognition techniques, but would discriminate against spectrum regions associated with chemical noise relative to those in which a peak might appear. 
       FIG. 9  shows a summary of the overall average Relative Standard Deviations (RSDs) as a function of proton chemical shift. These values were used as divisors to scale the MRS spectra at each respective chemical shift. The largest average RSDs appear as peaks in  FIG. 9 , representing chemical shift locations that had relatively high variance in signal values, but were not consistently associated with MRS peaks or proton NMR biomarkers of brain tissue. When used as a sequence of divisors in a weighting process, relatively high average RSD values in the weighting spectrum attenuate the signal values and relative low RSD values inflate the original MRS intensities at their respective chemical shift locations. 
     Variance weighting substantially increased the resolution of peaks in the MRS scans and produced distinguishable peaks in scans where previously the peaks had been barely observable. Further, variance weighting eliminated any remaining chemical shift variation and positioned most biomarker peaks at their expected locations. Provisionally identified biomarker peaks (Martinez-Bisbal el al, 2004) that appeared exactly at previously reported positions in this experiment included acetate (1.91 ppm); proline (2.00 ppm); glutamate (2.04 ppm); glutamine (2.14 ppm); valine (2.28 ppm); succinate and malate (2.39); N-acetyl aspartate (2.49 ppm); choline (3.19 ppm); ethanolamine, phenylalanine (3.12 ppm); taurine (3.26 ppm); β-glucose, taurine, and proline (3.42 ppm); β-glucose (3.46 ppm); and glycerol (3.46 ppm). Further, the weighting process preserved the relative peak intensity pattern associated with astrocytomas even though the weighting function was based on RSDs averaged for spectra of all available tissue types. 
     Example 3 
     Effects of MRS Spectrum Preprocessing on the Efficacy of Automated Diagnostic Methods 
     To assess the effects of MRS spectrum preprocessing on the efficacy of automated pattern recognition methods used to identify different tissue types based on patterns of biomarker peaks, the following experiment was conducted. 
     MRS scans obtained using the methods described in Example 1 were preprocessed and analyzed using automated pattern recognition techniques. Three preprocessing strategies were investigated in this experiment: 1) chemical shift re-calibration, 2) baseline correction, and 3) variance-weighting. Only the TE 35 ms scans were used for preprocessing evaluations. 
     The effectiveness of the preprocessing strategies on the diagnostic efficacy of the MRS spectra was assessed by comparing diagnostic results calculated using RESolve 1.2 (Hi-Res version) obtained from the Colorado School of Mines. A subset of the 92 MRS scans described in Table 2 of Example 1 was used for modeling and cross-validation experiments. The RESolve software provides several alternative types of pattern recognition; in this experiment, Principal Component and Discriminant Analysis was used to develop quantitative results. The 47 MRS scans omitted from the original MRS scan data set were used subsequently as an external validation set for comparing the two methods determined to yield the highest diagnostic efficacy. 
       FIG. 14  summarizes the results of a Principal Components and Discriminant Analysis performed by the RESolve 1.2 using minimally preprocessed MRS spectra with the spectra being normalized but otherwise unmodified prior to analysis.  FIG. 15  summarizes a similar analysis performed using pre-processed MRS spectra in which the spectra were subjected to normalization, recalibration, and variance-weighting prior to analysis. A comparison of  FIG. 14  with  FIG. 15 , shows that the preprocessing of the spectra categories reduced the separation of the data within the cluster for each particular tissue type and increased the separation distance between the clusters from different tissue types, thereby indicating that the diagnostic model derived using the preprocessed spectra discriminates more distinctly between the different tissue types. 
     Table 4 summarizes the results of the assessment of the diagnostic efficacy of MRS spectra that were preprocessed using various combinations of preprocessing strategies. Table 4 lists the cumulative predictive accuracy for classification among nine categories of tissue types in the four 92-scan data sets under left one out (LOO) cross-validation using all 380 data points of each MRS spectrum. Variability-weighting dramatically improved the diagnostic accuracy of the MRS spectra data relative to MRS spectra that were preprocessed using only normalization or only recalibration. A combination of normalization, recalibration, and variance-weighting resulted in the highest diagnostic efficacy of any of the preprocessing strategies assessed. 
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Diagnostic Efficacy of Pattern Recognition 
               
               
                 Methods Using Pre-Processed MRS Spectra 
               
            
           
           
               
               
               
            
               
                   
                   
                 Cumulative Predictive 
               
               
                   
                 Preprocessing Strategy 
                 Accuracy 
               
               
                   
                   
               
               
                   
                 Normalization only 
                 31.5% 
               
               
                   
                 Normalization + Recalibration only 
                 30.4% 
               
               
                   
                 Normalization + Variance Weighting + 
                 89.1% 
               
               
                   
                 Renormalization 
               
               
                   
                 Normalization + Recalibration + 
                 94.6% 
               
               
                   
                 Variance Weighting + Renormalization 
               
               
                   
                   
               
            
           
         
       
     
     Example 4 
     Sensitivity of the Efficacy of Automated Diagnostic Methods to the Number of Spectrum Data Points in the Diagnostic Model 
     To assess the sensitivity of the efficacy of a diagnostic model to the number of MRS spectra data points incorporated into the development of the model, the following experiment was conducted. 
     Two diagnostic models were constructed using the 92 MRS spectra data points that were preprocessed using normalization, recalibration, and variance-weighting, in which the nine tissue types were classified using left one out (LOO) cross-validation as described in Example 3. The first diagnostic model incorporated all 380 data points within each spectrum, as described in Example 3. The second diagnostic model incorporated a subset of 97 data points within each spectrum corresponding to the 97 biomarkers listed in Table 2 of Example 1 above. 
     An external validation of the diagnostic models was performed using the 47 MRS spectra reserved for the validation. The 47 spectra are listed in Table 2 of Example 1 above. All MRS spectra were subjected to preprocessing that included normalization, recalibration, and variance-weighting prior to analysis using the diagnostic models. 
       FIG. 16  summarizes the results of a Principal Components analysis performed using all MRS spectra, with the 47 validation spectra shown as unknown types. As shown in  FIG. 16 , the 41 validation spectra obtained from normal tissue appeared to cluster tightly over the normal tissue data obtained previously. The remaining six spectra (four obtained from oligodendroglioma tissue and two obtained from glioblastoma multiforme tissue) were situated among the abnormal tissue data obtained previously. 
     The two data models were used to diagnose the original 92 MRS scans used to develop the models as well as the 47 validation spectra into different tissue categories. The tissue categories predicted by the diagnostic models were compared to the known classification of each spectrum to assess the accuracy of each model. The accuracy of the predicted tissue type of the two models is summarized in Table 5. The use of the diagnostic model developed using the subset of biomarker data points from the model training set resulted in a predictive accuracy of 100% for the spectra within the external validation data set, compared to 95.7% accuracy obtained using all data from the spectra. 
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Comparison of Diagnostic Efficacy of Pattern Recognition 
               
               
                 Models Using Pre-Processed MRS Spectra 
               
            
           
           
               
               
               
            
               
                   
                 Cumulative Predictive Accuracy 
                   
               
            
           
           
               
               
               
            
               
                   
                   
                 Biomarker 
               
               
                 MRS Spectra 
                 Full Spectrum 
                 Spectrum Subset 
               
               
                 Analyzed 
                 (380 data points) 
                 (97 data points) 
               
               
                   
               
               
                 Model Training Set 
                 94.6% 
                 93.5%  
               
               
                 (n = 92) 
               
               
                 External Validation Set 
                 95.7% 
                 100% 
               
               
                 (n = 47) 
               
               
                   
               
            
           
         
       
     
     Example 5 
     Development of Tissue Category Subclasses Using Automated Diagnostic Methods 
     To assess development of an automated diagnostic method that categorized subclasses of tissue types, the following experiment was conducted. 
     A subset of the scans used for model training summarized in Table 2 of Example 1 were used to develop a diagnostic model using methods similar to those described in Example 3. In this experiment, only the fourteen astrocytoma scans and the 20 glioblastoma multiforme scans were used to develop the diagnostic model. The astrocytoma scans were divided into two categories corresponding to grade 2 or grade 3. The glioblastoma multiforme scans were assigned to a category corresponding to grade 4; glioblastoma multiforme is an abnormal astrocytoma tissue type also known as grade 4 astrocytoma. The diagnostic model developed using this method has an R 2  of 0.82. 
     The results of this experiment indicated that the method of developing diagnostic models using preprocessed MRS spectra may be useful in discriminating between different grades within the same tissue category. 
     It should be understood from the foregoing that, while particular embodiments have been illustrated and described, various modifications can be made thereto without departing from the spirit and scope of the invention as will be apparent to those skilled in the art. Such changes and modifications are within the scope and teachings of this invention as defined in the claims appended hereto. 
     References  
     
         
         1. Martinez-Hisbal, M. Carmen; Marti-Bonmati, Luis; Piquer, Josè; Revert, Antonio; Ferrer, Pilar; Llácer, Josi L.; Piotio, Martial; Assemat, Olivier; and Celda, Bernardo; (2004) “IH and I3C HR-MAS spectroscopy of intact biopsy samples ex vivo and in vivo 1H MRS study of human high grade gliomas”, NMR Biomed. 2004; 17:191-205. 
         2. Webb P. B., Sailasuta N., Kohler S. J., Raidy T., Moats R. A., Hurd R. E. (1994) “Automated single-voxel proton MRS: technical development and multisite verification.” Magn. Reson. Med. 31:365-373.