|
Size: 4750
Comment:
|
Size: 5299
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| == FreeSurfer Tutorial: Sample Data == | '''Index''' |
| Line 5: | Line 5: |
| A [[http://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_public_distribution.README.txt|public distribution data set]] is available to run the tutorials. It contains 40+ subjects, and occupies about 11G of disk-space after download and decompression. There are two download methods: using a web browser, or using the ftp application. The ftp application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size.There are also two tar files associated with the tutorial on the integration of FreeSurfer and FSL/FEAT. | <<TableOfContents>> |
| Line 7: | Line 7: |
| === Download using the FTP application === | == FreeSurfer Tutorial Datasets == ## The data set for the Freesurfer tutorials comes in two forms, a "Lightweight" version and a "Full" version. |
| Line 9: | Line 10: |
| At your terminal, type '''ftp surfer.nmr.mgh.harvard.edu'''. Login as '''anonymous''' and use your email address as the password. | ## * The "Lightweight" version contains only the files required to run the commands of the !FreeSurfer tutorial. It has all the required input and output data, but lacks the other files that would normally be present when performing a recon. People who just want a quick easy way to run the commands in the tutorial should download this data set. |
| Line 11: | Line 12: |
| Example login: | ## * The "Full" version contains all the files that would normally be present when performing recons. Because of the numerous subjects involved with the tutorials, the full data set is quite large (~60Gigs). People who want to go into more depth than that which is covered in the tutorials should download this data set. ## == Lightweight version == ## Use the following link to download the lightweight version of the tutorial data: ## . [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz|tutorial_data.tar.gz]] ## Once the download is complete, uncompress the data file - this usually this can be done by simply double-clicking. In order to do the tutorials, users must define an environment variable called '''TUTORIAL_DATA''' which is set to the location of the extracted data. For example: ## {{{ ## $> export TUTORIAL_DATA=/home/username/Downloads/tutorial_data ## $> ls $TUTORIAL_DATA ## buckner_data fsfast-functional ## diffusion_recons fsfast-tutorial.subjects ## diffusion_tutorial long-tutorial ## }}} ## You are now ready to start the [[Tutorials|Freesurfer tutorials]]. ## == Full version == The full data for the [[Tutorials|tutorials]] consists of several data sets: * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz|buckner_data-tutorial_subjs.tar.gz]]: the main 'recon-all' stream subject data processing (size: ~16GB uncompressed). * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.tar.gz|long-tutorial.tar.gz]]: the longitudinal tutorial (size: ~16GB uncompressed) * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz|fsfast-tutorial.subjects.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz|fsfast-functional.tar.gz]]: the FS-FAST tutorial data set (size: ~5.6GB uncompressed & ~9.1GB uncompressed, respectively) * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.tar.gz|diffusion_recons.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.tar.gz|diffusion_tutorial.tar.gz]] - the diffusion and Tracula tutorial data sets Also, if you only want to get started with the basics of !FreeSurfer, you need only download the buckner_data set. This will allow you to do the following tutorials: * [[FsTutorial/OutputData_freeview|Intro to FreeSurfer Output]] * [[FsTutorial/TroubleshootingData|Troubleshooting FreeSurfer Output]] * [[FsTutorial/GroupAnalysis|Group Analysis via command-line]] * [[FsTutorial/QdecGroupAnalysis_freeview|Group Analysis via GUI]] * [[FsTutorial/AnatomicalROI|ROI Analysis]] * [[FsTutorial/MultiModal_freeview|Multimodal Analysis]] === Installation === ==== Uncompress the files ==== Once the dataset(s) have been downloaded, uncompress and install with the following command run from a terminal window. |
| Line 14: | Line 53: |
| $ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220 surfer.nmr.mgh.harvard.edu FTP server (Version wu-2.6.2-15.7x.legacy) ready. Name (surfer.nmr.mgh.harvard.edu:fsurfer): anonymous 331 Guest login ok, send your complete e-mail address as password. Password: 230 Guest login ok, access restrictions apply. Remote system type is UNIX. Using binary mode to transfer files. ftp> |
tar -xzvf <filename>.tar.gz |
| Line 25: | Line 55: |
| Replacing <filename> with the name of the file downloaded. The downloaded .tar.gz files can then be deleted. | |
| Line 26: | Line 57: |
| The tutorial datasets are found in the pub/dist directory: {{{ ftp> cd pub/dist }}} |
==== Set variables to point FreeSurfer to data ==== |
| Line 31: | Line 59: |
| The troubleshooting and group study analysis tutorials require the '''buckner_data-tutorial_subjs.tar.gz''' and '''buckner_data-tutorial_subjs-group_analysis_tutorial.tar.gz''' downloads, which are 6.5GB compressed (11GB decompressed): {{{ ftp> get buckner_data-tutorial_subjs.tar.gz ftp> get buckner_data-tutorial_subjs-group_analysis_tutorial.tar.gz }}} To get the FSL-FEAT tutorial data {{{ ftp> get fbert-feat.tar.gz ftp> get bert.recon.tar.gz }}} Now exit the ftp application: {{{ ftp> quit }}} === Download using the web browser === Some web browsers seem to have difficulty downloading files greater than 4GB in size, but if you would like to attempt the download using your browser, then the one necessary file is listed next (click on the .tar.gz filename to download). The troubleshooting and group study analysis tutorials require these downloads: * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz|buckner_data-tutorial_subjs.tar.gz]] * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-group_analysis_tutorial.tar.gz|buckner_data-tutorial_subjs-group_analysis_tutorial.tar.gz]] The FSL-FEAT tutorial require these: * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.tar.gz|fbert-feat.tar.gz]] * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tar.gz|bert.recon.tar.gz]] === Installation === Once the file is downloaded (via either ftp or web browser), move the file(s) to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following commands: |
Once the download is complete you may uncompress the tar files. In order to do the tutorials, users must define an environment variable called '''TUTORIAL_DATA''' which is set to the location of the extracted data. For example: |
| Line 63: | Line 62: |
| tar xzvf buckner_data-tutorial_subjs.tar.gz tar xzvf buckner_data-tutorial_subjs-group_analysis_tutorial.tar.gz |
export TUTORIAL_DATA=/home/username/Downloads/tutorial_data ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial |
| Line 66: | Line 68: |
| You are now ready to start the [[Tutorials|Freesurfer tutorials]]. | |
| Line 67: | Line 70: |
| The downloaded .tar.gz files can then be deleted. | {{{ (bash) export TUTORIAL_DATA=<absolute_path_to_tutorial_data_directory> |
| Line 69: | Line 74: |
| To setup the environment variable SUBJECTS_DIR to point to the tutorial data, type the following command or include in your .cshrc or .tcshrc file: {{{ source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/subjects.csh |
(csh) setenv TUTORIAL_DATA <absolute_path_to_tutorial_data_directory> |
| Line 73: | Line 77: |
| '''Note:''' The tutorial references the {{{TUTORIAL_DATA}}} variable, which is the root directory containing the tutorial data (ie. the directories 'buckner_data', 'long-tutorial', 'fsfast-functional', etc.). | |
| Line 74: | Line 79: |
| '''Note:''' If you are within the NMR Center, because the default $FREESURFER_HOME is shared, you will not be able to copy your data to $FREESURFER_HOME/subjects. Instead, copy the subject data to a location where you have space, and set the SUBJECTS_DIR environment variable to point to that. You may have to make adjustments throughout the tutorial wherever it refers to $FREESURFER_HOME/subjects (which is equivalent to your $SUBJECTS_DIR). | == FreeSurfer Tutorial Datasets 5.1/5.3 == |
| Line 76: | Line 81: |
| The tutorial will also instruct you to set the SUBJECTS_DIR when appropriate. === Additional group study data === There is an additional data set available upon which further group study analysis could be conducted. It is composed of the 40 subjects from which the tutorial's group study component was created. The data set is the full Freesurfer reconstruction of the 40 subjects (conducted using stable v3.0.2). It is 10.5GB compressed, and 18GB decompressed. It is named '''buckner_data-group_study.tar.gz'''. Also, there is the file '''buckner_data-raw_dicoms.tar.gz''', which, as indicated by the name, contains the original DICOM files for the subjects. Be sure to [[http://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_public_distribution.README.txt|read these notes.]] === FSL-FEAT Tutorial Data === {{{ cd $SUBJECTS_DIR tar xvfz bert.recon.tar.gz cd /place/for/functional/data tar xvfz fbert-feat.tar.gz }}} |
* [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-5.3.tar.gz|buckner_data-tutorial_subjs-5.3.tar.gz]] * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutoriaL-5.3.tar.gz|long-tutorial-5.3.tar.gz]] * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects-5.3.tar.gz|fsfast-tutorial.subjects-5.3.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz|fsfast-functional-5.3.tar.gz]] * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons-5.3.tar.gz|diffusion_recons-5.3.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial-5.3.tar.gz|diffusion_tutorial-5.3.tar.gz]] |
Index
Contents
FreeSurfer Tutorial Datasets
The full data for the tutorials consists of several data sets:
buckner_data-tutorial_subjs.tar.gz: the main 'recon-all' stream subject data processing (size: ~16GB uncompressed).
long-tutorial.tar.gz: the longitudinal tutorial (size: ~16GB uncompressed)
fsfast-tutorial.subjects.tar.gz & fsfast-functional.tar.gz: the FS-FAST tutorial data set (size: ~5.6GB uncompressed & ~9.1GB uncompressed, respectively)
diffusion_recons.tar.gz & diffusion_tutorial.tar.gz - the diffusion and Tracula tutorial data sets
Also, if you only want to get started with the basics of FreeSurfer, you need only download the buckner_data set. This will allow you to do the following tutorials:
Installation
Uncompress the files
Once the dataset(s) have been downloaded, uncompress and install with the following command run from a terminal window.
tar -xzvf <filename>.tar.gz
Replacing <filename> with the name of the file downloaded. The downloaded .tar.gz files can then be deleted.
Set variables to point FreeSurfer to data
Once the download is complete you may uncompress the tar files. In order to do the tutorials, users must define an environment variable called TUTORIAL_DATA which is set to the location of the extracted data. For example:
export TUTORIAL_DATA=/home/username/Downloads/tutorial_data ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial
You are now ready to start the Freesurfer tutorials.
(bash) export TUTORIAL_DATA=<absolute_path_to_tutorial_data_directory> (csh) setenv TUTORIAL_DATA <absolute_path_to_tutorial_data_directory>
Note: The tutorial references the TUTORIAL_DATA variable, which is the root directory containing the tutorial data (ie. the directories 'buckner_data', 'long-tutorial', 'fsfast-functional', etc.).