OpenLLM-France/wikimedia huggingface dataset:
# MINC/Atlases

Atlases are marvellous things and everyone should have one.
Atlases/History - A short history of the various atlases that have been produced at the BIC (McConnell Brain Imaging Center, Montreal Neurological Institute).

## ICBM152 Linear

This is a linear average.
In 2001, within the context of the ICBM project (19) a concerted effort was undertaken by three sites (MNI, UCLA, RIC) to collect a set of full- brain volumetric images from a normative population specifically for the purposes of generating a model. 152 new subjects were scanned using T1, T2 and PD sequences as the MNI’s part of the ICBM project using a specific protocol (27). These images were acquired at a higher resolution than the original average 305 data and exhibit improved contrast due predominately to advances in imaging technology. Each individual was linearly registered to the average 305 and a new model was formed. In total, three models were created at the MNI, the ICBM152_T1, ICBM152_T2 and ICBM152_PD from 152 normal subjects. This resulting model is now known as the ICBM152 (although the model itself has not been published). One advantage of this model is that it exhibits better contrast and better definition of the top of the brain and the bottom of the cerebellum due to the increased coverage during acquisition.
The entirely automatic analysis pipeline of this data also included grey/white matter segmentation via spatial priors (41). The averaged results of these segmentations formed the first MNI parametric maps of grey and white matter. The maps were never made publicly available in isolation but have formed parts of other packages for some time including SPM, FSL AIR and as models of grey matter for EEG source location in VARETTA and BRAINWAVE.
Again, as these models are an approximation of Talairach space, there are differences in varying areas, to continue our use of origin shift as an example, the ICBM models are approximately
152: – +3.5mm in Z and +-co-ordinate -3.5mm and 2.0mm in Y as compared to the original Talairach origin.
In addition to the standard analysis performed on the ICBM data, 64 of the subjects data were segmented using model based segmentation. 64 of the original 305 were manually outlined and a resulting parametric VOI atlas built.
The native data from these acquisitions was 256x256 with 1mm slices. The final image resolution of this data was 181x217x181 with 1mm isotropic voxels.
And here is a link to it: ICBM152 linear model

## Latest Version: ICBM152 Symmetric Non Linear 2009c

Official Location of files

## Which should I use?

ICBM152 NonLinear: If you are fitting an individual to model and do not care about left/right comparisons
# The future of MINC

MINC is a complex, powerful image file format for medical images that includes a standard API to ensure that all files read/written conform to the MINC standard. MINC is also a collection of software tools for qualitative and quantitative medical image analysis that has been developed over the past 20 years. Unfortunately, MINC is difficult to install and the learning curve is steep for new users.
Our goal is to guarantee a future for MINC (and the MINC tools) in the face of competing file formats and software packages by simplifying the installation and use of the MINC libraries and tools.
This book/page will serve as a location to discuss difference aspects of MINC that need to be changed or improved and will also serve to record the history of the decision process of these changes (circa 2011).
These changes were initiated by a discussion on the GEEKS list, and then in telephone conference held Feb 23, 2011 were we discussed these notes. The goals of this tconf were to identify some of the issues involved and the majors steps needed to move forward. The outcome of this call was the creation of a list of actions that we needed to address to start the process of improving MINC.
Some of the actions require discussion amongst the interested parties:
DevelopmentShift - Discussion of where to shift the development environment
# Authors of MINC

Many People have contributed to MINC over the years. Peter Neelin originally conceived and wrote MINC in about 1992, here is a list of others who have contributed parts of MINC proper (in alphabetical order).
* Leila Baghdadi - MINC2 coding
* Louis Collins - mni_autoreg, classify and others
* Mishkin Derakhshan - many bugfixes
* Vladimir Fonov - many bugfixes
* Andrew Janke - Maintenance, binary packaging, documentation
* Jason Lerch - brain view and other surface things
* Dave McDonald - conglomerate, register, Display
* Claude LePage - many bugfixes to many packages
* Steve Robbins - surface code, Debian packaging
* John Sled - N3
* Jussi Tohka - PVE
* Bert Vincent - coded MINC2
* Mark Wolforth (wolforthpet.mni.mcgill.ca) - contributed to pages linked at MINC/Tools/emma
* Greg Ward (gregbic.mni.mcgill.ca) - contributed to pages linked at MINC/Tools/emma
* Alex Zijdenbos - Classify

# How to reference MINC

If you need to reference MINC itself in a paper, the best option is to use one of these two web links
Some standard text you might include:
Medical Imaging NetCDF (MINC) is a medical imaging data format and associated set of tools and libraries developed at the Montreal Neurological Institute (MNI) and freely available online
References for particular tools are given below

## classify

classify is a segmentation package that includes the classify_clean script.
The tool classify_clean, which is used to classify stereotaxic MINC volumes, involves a Bayesian labeling scheme and a set of standard sample points to compute an initial volume classification. This classification is then employed to purge incorrect tag points from the standard set, yielding a custom set of labels for the particular subject. Finally, this tag point set is used by an artificial neural net classifier to classify the volume (Zijdenbos et al., 1998).
Zijdenbos, A., Forghani, R., Evans, A., 1998. Automatic quantificationof MS lesions in 3D MRI brain data sets: validation of INSECT. Medical Image Computing and Computer-Assisted Interventation—MICCAI'98, pp. 439–448
# Managing your business with anyPiece/WYSIWYG Web editor/Web designer or programmer/Create new web template
## Create new web template

* Go to WebEditor Manager
* If you company not have any website, you will see Website dialog, but if your company already have website, click on WebSite select box then choose Add New WebSite.
* Enter Website Name then click OK
* If you are doing correctly, you will be able to see your web site name under website select box.

### Tutorial

* Go to WebEditor Manager
* Create website by select Add New Website on Website select box
* Enter website name as “example website”
* Click OK
# Managing your business with anyPiece/WYSIWYG Web editor/End user/Setup extRouter
## System requirement

* Required ASP.NET 4
* Required read and write for the web application as we will need to write and update files

## Technical knowledge for the setup personnel

* Know how to FTP
* Know how to edit web.config using notepad
* Know how to play around with IIS

## Basic information needed

* WebSiteID
* Token
* Password
* WebURL for API

## Setup guide

* [Download the extRouter from anyPiece website
* Extract the file and put it to your server of choice
* Change the web.config base on the data your have in #Basic information needed. Please refer to #Web.config setup if you need further help.
* Type the flush command to your website. Example; http://www.mywebsite.com/flush

## Web.config setup

Your web.config should look like below when you download
* Change "WebSiteID" value
* Change "Token" value
* Change "Public_Key" value
* Change "webservice_url" value

## Troubleshooting
### Why am I getting Invalid Token?

As the designer can block or the token have been changed due to changes, please contact your designer or re-seller for new API code.

### Why am I getting not able to write?

Please ensure your folder read/write permission to the network service of ASPNET_IIS
# List of tag

As we can't really remember all the tag, we will try our best to update that tag that available for usage over here.

## Master page only
### Content tag

* Use by master page to replace the content with sub page

## General
### Comment/remark

* This syntax is usually used by the developer to remark unwanted code during editing. Some of the most common area would be loading the jquery. As in anyPiece platform, jQuery is loaded up by default. If its double load, it will crash and kill the system. Please refer to the sample below.
# Manchester Field Course 2009

This document is a collaborative report generated in connection with the a field course to Manchester(UK) and surrounding landscapes. The participants in the field course are Master students of geography from Roskilde University Denmark. The document is a combination of a desktop work before the field course and observations for the fieldwork period (14 days) The subjects covered in this document are a combination of mandatory subjects defined by the course teachers and subjects chosen by the students. We have chosen the Wikibook format in order to facilitate co-authoring with people and organizations outside the field course group.

## Contents

* Course Program
** Program preparation: An overview of the preparation period
** Program field: An overview of the field work period and course diary
* Mandatory subjects
** Classical industrial production: Classical industrial production in Manchester
** Information/Media industry: Information/Media industry in Manchester
** Experience Economy: Experience Economy in Manchester
** Urban reproduction: Functional mapping of Urban reproduction in Manchester
** Landscape Character Assessment
** rural regeneration
** Nature reserve management
* Student projects
** New urbanism
** Event management
** Strategic planing
** Planing from a child perspective
General links General links about Manchester
# Manchester Field Course 2009/Planing from a child perspective

Manchester Field Course
Description: The project will examine how young people interact the in Trafford Center nearby Manchester. On the basis of the specific history and social context of the center we will thereby try to get a socio-spatial understanding of the codexes and rules that is connected to the Trafford Center. With an ethnographical view we will try to get an understanding of how the young people interact and shape their own space within the center.
Problem statement:
How do young people shape their own space within the Trafford Center?
* How do they interact?
* Which cultures is represented?
* How often do these young people come here? From Where? And Why?
Tags: Control, regulation, commercialization, teenage culture
# Manchester Field Course 2009/Program field

Preliminary program:
Day 1 Arrival and "taking in Manchester"
Day 2 Classical industrial production
Day 3 Information/Media industry
Day 4 Experience Economy
Day 5 Urban reproduction (functional urban mapping)
Day 6 Project work
Day 7 Landscape Character Assessment
Day 8 Rural renewing
Day 9 Nature reserve management
Day 10 Project work
Day 11 Project work
Day 12 Project work
Day 13 Project work
Day 14 Project work
# Web editor introduction

To start with the most fundamental, we will introduce you to some of the most basic information
* Web Editor Manager (WEM) - This is the core of the web editor engine. You will be handling all the static-image, css and javascript mostly from here. This section usually will not be touch by the end user. To access this web maanger, you can go to [www.anypiece.com/module/webeditormanager]
* Web Editor - This is the center piece for end user to edit and update their website

## Basic tutorial

* Step 1: Create new web template
* Step 2: Create page template
* Step 3: Create page
* Step 4: Test out the page using ext router
* Step optional: Add static files and javascript

## Advance tutorial

* Work with anyPIECE API
* Work with google spreadsheet (only application with version 2.2)
# Managing your business with anyPiece/WYSIWYG Web editor/Web designer or programmer/Work with google spreadsheet
## Prerequisite

* Please make sure your form have following field configure into your form
| Field Name | Type | Explanation |
| spreadsheet_name | hidden | The spreadsheet that we will use. It must be created up front. |
| sheet_name | hidden | Use to check on the sheet that we will use to insert the data |
* Please configure the extrouter web.config as per below
** To get this client id and client secret, please visit [Google oAuth]
* Please configure the refresh token
** Refresh token would be the key token that will enable the system to upload data to your spreadsheet without your user name and password
** To get refresh token, type http://yourwebsite.com/google_spreadsheet. You will be ask to login under your google mail account
* Since we have updated one of the component (newton), please update the web.config to below
* Make sure that you have created the spreadsheet into your google drive with the same name as spreadsheet_name

## Setup guide on the form

* Create all the three hidden field as per stated in the Prerequisite
* Put the form action to "google_spreadsheet" and method to "post"
* Please make sure all the form have the field which will be sent over from the form to google docs. If there is a missing field, you will get an error like below.
* If you are doing correctly, the system will push the screen to success_url which you have configure in the hidden field
# Manchester Field Course 2009/General links

Manchester travel guide on Wikivoyage
# HydroGeoSphere/Observation Wells and Points

The following instructions are used to output hydraulic head, saturation (if variablysaturated) and nodal fluid flux at a single node or a group of nodes lying on a line.
Output is written to a TECPLOT-formatted file called prefixo.observation_well_flow.-obs_well_name.dat.
If the problem is formulated as a dual continuum then extra columns of output will be produced with the dual continuum head, saturation (if variably-saturated) and fluid flux. If the node is not a dual continuum node, no data values (currently -999.0) will be written instead.
If the problem is formulated with a surface flow domain then extra columns of output will be produced with surface flow head and fluid flux. If the node is not a surface flow node, a no data value (currently -999.0) will be written instead.
These instruction do not affect the flow solution.

## Make observation point

* well_name Descriptive name for the well up to 40 characters.
* x1, y1, z1 xyz-coordinates of the observation point.
The node closest to this point will be flagged as an observation point node.
Data for each timestep in the flow solution is written as one line in the output file. Each line contains the time and then the porous medium hydraulic head, saturation (if variably-saturated), fluid flux, node coordinates and node number.

## Make node observation point

* well_name Descriptive name for the well up to 40 characters.
* nnumber The number of the node to be made an observation point.
This node will be flagged as an observation point node.
Data for each timestep in the flow solution is written as one line in the output file. Each line contains the time and then the porous medium hydraulic head, saturation (if variably-saturated), fluid flux, node coordinates and node number.

## Make observation well

* well_name Descriptive name for the well up to 40 characters.
* x1, y1, z1 xyz-coordinates of one end of the observation well.
* x2, y2, z2 xyz-coordinates of the other end of the observation well.
Element face edges (i.e. segments) which form the shortest path between the two nodes closest to the end points of the well (i.e. x1, y1, z1 and x2, y2, z2) will be chosen to produce output.
Each timestep in the flow solution represents a Tecplot zone in the output file, and each zone contains one line per observation well node. Each line contains the porous medium hydraulic head, saturation (if variably-saturated), fluid flux, node coordinates and node number.
Note that fluid fluxes at internal nodes are currently reported as zero unless they are constant head or specified flux nodes.
# HydroGeoSphere/Matrix Solver

The matrix solution procedure consists of three phases: initialization, preconditioning and solution. The instructions presented here can be used to control the preconditioning and solution phases in order to increase the efficiency of the model.

## Preconditioning suggestions

The default preconditioning scheme is level-based factorization without red/black system reduction. Improving model performance requires a good understanding of these options, and so if you are unsure you should just use the default settings. However, if you decide to experiment with the solver preconditioning parameters, here are a few suggestions for doing so:
* For transient, simple (i.e. small number of nodes) problems, level-based preconditioning works better, because the static data structure analysis does not need to be done for each time step.
* For steady state or complex problems, drop tolerance preconditioning works better, because WATSIT spends most of its time in the solution phase, not the preconditioning phase.
* For a very smoothly varying solution (e.g. a weakly stressed, homogeneous property field) red/black reduction will speed convergence.

## Level of fill

* level Level of fill.
Assigns the level of fill to be preserved in level-based factorization, which defaults to 0. If drop tolerance preconditioning is used, this value is not used.

## Red black reduction

Tells the solver to use red black reduction. This can be used either using level-based or drop tolerance preconditioning.

## Drop tolerance preconditioning

Tells the solver to use drop tolerance preconditioning. This will remove elements based on how small they are. The default threshold is 0.1.

## Drop tolerance threshold

* thres Drop tolerance threshold.
Assign a new drop tolerance threshold.
Once the preconditioning phase is complete, the matrix can be solved using several acceleration techniques. The following command can be used to change the solver procedure:

## Solver acceleration technique

* iaccel Type of acceleration to use.
Assigns a new value for the acceleration technique for the linear solver, which defaults to 3 (CGSTAB-P). Appropriate values are 0 (CG, for symmetric matrices only), 1 (OrthoMin), 2 (CGS), 3 (CGSTAB-P) or 4 (GMRES). If unsure, don’t use this command.

## No matrix scaling

Tells the solver not to use matrix scaling preconditioning.
# HydroGeoSphere/Manipulating the 3-D Grid
## Tilt grid x

Tilts a grid by 90$^o$around the x-axis. This is especially suitable in conjunction with the instruction read slice which reads a two-dimensional grid (parallel to the xy-plane) in gms format.

## Tilt grid y

As above but for the y-axis.

## Adapt grid to fractures

* adapt_g2f_mode An integer value indicating how the grid is adapted to inclined fractures.
If block elements are used, two inclined fractures may intersect in the middle of an element instead of on a grid node, so the fractures will not be connected unless additional nodes are specified.
Acceptable values for the variable adapt_g2f_mode and the actions taken in each case are:
    0 No action is taken.
    1 New grid lines are added.
    2 The block element is substituted by four prisms.
    3 Inclined faces are not selected in the block element where the problem occurs.
The default value is 1.
# HydroGeoSphere/Output

During execution, grok and HydroGeoSphere create many output files, for which a complete list with brief descriptions can be found in Appendix B. Here, we will discuss in more detail the output which is of most interest to the user.

## Output files

The main mechanism for generating output from HydroGeoSphere is through the use of the Output times instruction. For each output time defined by the user, there will be a problem-dependent set of output files which will be generated automatically. Here is a partial list of the files which were created by the verification problem described in Section 4.5.2:
As you can see, file names are made up of the problem prefix, in this case f_cd, a descriptor, for example o.concentration.Radium. and a 3-digit number such as 001, which relates the data contained in the file to an output time number. Note that for output time number 001, there are quite a few more output files than for number 002. This is because the flow solution in this case is steady-state, and so it is fully described by one set of output. For timestep 002, only variables which have changed are output, in this case the concentrations of the 3 species in the transport solution. Finally, the set of files which gets generated is problem-dependent, and so certain types of files may or my not appear. For example, since this problem has discrete fractures, we are seeing some fracture velocity and aperture output.
In order to conserve disk space and increase the efficiency of file I/O, these files are all stored in binary format, so they can not be viewed with a standard text editor. However, through the use of the post-processing tool HSPLOT, which is described in Section E, it is possible to create ascii versions of the data contained in these files which are also compatible with the third-party visualization tools TECPLOT and GMS.

## Time output format

By default, simulation time is written in listing and output files in a fixed format using the FORTRAN F format descriptor f17.5, which is not suitable for outputting times greater than 999,999 or less than 0.00001. If you prefer to use scientific notation, you can choose it using the instruction:
       Time output scientific format
The other option is to use the FORTRAN G format descriptor (i.e. general format) in which a mix of fixed and scientific format is used depending on the magnitude of the output. If you prefer this notation, you can choose it using the instruction:
       Time output general format
Since these instructions can be used in the debug.control file (see Section C), it might sometimes be usefult to switch back to fixed format. To do so, use the instruction:
       Time output fixed format

## Mass balance output format

Similarly, mass balance output can be controlled by the instructions:
       Mass balance output scientific format
and
       Mass balance output general format
       Mass balance output fixed format
# HydroGeoSphere/Nodal Flux Head Constraints

The old instructions Specified volumetric flowrate and Specified volumetric flowrate, head constrained are no longer used, as they are covered by the boundary condition type Nodal flux described below. If you want to force the nodal flux to operate within a specified hydraulic head range, you can do so using the following instruction:

## Nodal flux head constraints

* bc_constraint_1, bc_constraint_2 Minimum and maximum constraining head values for positive nodal flux (i.e. inflow).
* bc_constraint_3, bc_constraint_4 Minimum and maximum constraining head values for negative nodal flux (i.e. outflow).
If the nodal flux is positive, and the head at the node is less than bc_constraint_1, then the flux will be applied until such time as the head at the node exceeds bc_constraint_2. Once the head at the node exceeds bc_constraint_2, then the flowrate will be set to zero until such time as the head at the node drops below bc_constraint_1.
If the flowrate is negative, and the head at the node is greater than bc_constraint_3, then the flowrate will be applied until such time as the head at the node drops below bc_constraint_4. Once the head at the node drops below bc_constraint_4, then the flowrate will be set to zero until such time as the head at the node exceeds bc_constraint_3.