|
Size: 4696
Comment:
|
Size: 7032
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| == FreeSurfer Tutorial: Sample Data == | == FreeSurfer Tutorial Datasets == |
| Line 5: | Line 5: |
| The data for the [[FsTutorial| tutorials]] consists of several data sets: * buckner_data-tutorial_subjs.tar.gz ~16GB uncompressed - the main 'recon-all' stream subject data processing ([[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt|here is the md5sum]]) * long-tutorial.tar.gz ~16GB uncompressed - the longitudinal tutorial * fsfast-tutorial.subjects.tar.gz ~5.6GB uncompressed and fsfast-functional.tar.gz ~9.1GB uncompressed - the FS-FAST tutorial data set * diffusion_recons.tar.gz and diffusion_tutorial.tar.gz - the diffusion and Tracula tutorial data sets * fbert-feat.tgz and bert.recon.tgz - tutorial on the integration of FreeSurfer and FSL/FEAT |
The Freesurfer tutorial dataset comes in two forms, a "light weight" version and a "full" version. |
| Line 12: | Line 7: |
| The wget application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size. '''Mac OS NOTE:''' use '''curl -O''' in place of '''wget'''. | * The "light weight" version of the data set contains only the files required to run the commands of the free surfer tutorial. It has all the required input and output data, but lacks the other subject data 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. * The "full" version of the data set 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. People who want to go into more depth than that which is covered in the course and the tutorials should download this data set. == FreeSurfer Tutorial Datasets - light weight version == Use the following link to download the light weight 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. To run the tutorials, simply source Freesurfer, then set an environment variable called '''TUTORIAL_DATA''': {{{ (bash) <source_freesurfer> export TUTORIAL_DATA=<path_to_tutorial_data> (csh) <source_freesurfer> setenv TUTORIAL_DATA <path_to_tutorial_data> }}} You are now ready to start the [[FsTutorial| Freesurfer tutorials]]. == FreeSurfer Tutorial Datasets - full version == The full data for the [[FsTutorial| tutorials]] consists of several data sets: * 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/buckner_data-tutorial_subjs.md5sum.txt|Here is the md5sum]]. * 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 * fbert-feat.tgz & bert.recon.tgz - tutorial on the integration of !FreeSurfer and FSL/FEAT 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]] |
| Line 14: | Line 50: |
| The wget application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size. '''Mac OS NOTE:''' Use '''curl -O''' in place of '''wget'''. | |
| Line 15: | Line 52: |
| Open a terminal, change to a directory where you know you have at least 100GB of space. To download, type: | Open a terminal, create a directory called {{{tutorial_data}}} where you know you have at least 100GB of space, and {{{cd}}} into that directory. To download, type: |
| Line 27: | Line 64: |
| The wget application will handle poor connections, and retry if it is having problems. A failed download can be restarted by adding the -c flag to wget, which will cause it to continue from the point where a partial download stopped. Notice the commands have the ampersand, so you can run all these commands at once (although the wget output will be hard to decipher, so an alternative is to run each without the ampersand in a separate terminal). Goto the Installation section below once the files are downloaded (this will likely take several hours). If you want to verify the md5sum, the md5sum for each of these files is found in files named *.md5sum.txt [[http://surfer.nmr.mgh.harvard.edu/pub/data/|in this directory]] or get them this way: | This download will likely take several hours. The wget application will handle poor connections, and retry if it is having problems. A failed download can be restarted by adding the -c flag to wget, which will cause it to continue from the point where a partial download stopped. Notice the commands have the ampersand, so you can run all these commands at once (although the wget output will be hard to decipher, so an alternative is to run each without the ampersand in a separate terminal). Go to the Installation section below once the files are downloaded. ==== Optional Verification Step ==== If you want to verify the files transferred correctly using md5sum, the md5sum for each of these downloads can found in files named *.md5sum.txt [[http://surfer.nmr.mgh.harvard.edu/pub/data/|in this directory]] or get them this way: |
| Line 40: | Line 82: |
| You will want to ensure that these md5sum's match what you find when you run md5sum on your own local downloads. | You will want to ensure that these md5sum's match what you find when you run md5sum on your own local downloads. If they do not match, the file transfer may have been faulty or there may have been a disk error. '''Mac OS NOTE:''' Use '''md5 -r''' to get the same results as '''md5sum'''. More on md5sum can be found [[http://www.techradar.com/us/news/computing/pc/how-to-verify-your-files-in-linux-with-md5-641436|here]]. |
| Line 43: | Line 85: |
Once the files are downloaded, move the file(s) to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following commands: |
==== Uncompress the files ==== Once the dataset(s) have been downloaded, uncompress and install with the following command run from a terminal window. |
| Line 50: | Line 92: |
| Replacing of course <filename> with the name of each file downloaded. The downloaded .tar.gz files can then be deleted. | Replacing <filename> with the name of the file downloaded. The downloaded .tar.gz files can then be deleted. |
| Line 52: | Line 94: |
| 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: | ==== Set variables to point FreeSurfer to data ==== To setup the environment variable {{{SUBJECTS_DIR}}} to point to the tutorial data, type the following commands every time you open a new terminal window. Alternatively, you can include the below commands in your .cshrc or .tcshrc file so these variables are automatically set every time you open a new terminal window: |
| Line 54: | Line 97: |
| setenv TUTORIAL_DATA $FREESURFER_HOME/subjects setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs/ |
(bash) export TUTORIAL_DATA=<absolute_path_to_tutorial_data_directory> (csh) setenv TUTORIAL_DATA <absolute_path_to_tutorial_data_directory> |
| Line 58: | Line 104: |
| '''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 TUTORIAL_DATA and SUBJECTS_DIR environment variables 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). The tutorial will also instruct you to set the SUBJECTS_DIR when appropriate. The tutorial references the TUTORIAL_DATA var, which is the root directory containing the tutorial data (ie. the directories 'buckner_data', 'long-tutorial', 'fsfast-functional', etc.). |
'''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.). |
FreeSurfer Tutorial Datasets
The Freesurfer tutorial dataset comes in two forms, a "light weight" version and a "full" version.
- The "light weight" version of the data set contains only the files required to run the commands of the free surfer tutorial. It has all the required input and output data, but lacks the other subject data 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.
- The "full" version of the data set 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. People who want to go into more depth than that which is covered in the course and the tutorials should download this data set.
FreeSurfer Tutorial Datasets - light weight version
Use the following link to download the light weight version of the tutorial data:
Once the download is complete, uncompress the data file - this usually this can be done by simply double-clicking. To run the tutorials, simply source Freesurfer, then set an environment variable called TUTORIAL_DATA:
(bash) <source_freesurfer> export TUTORIAL_DATA=<path_to_tutorial_data> (csh) <source_freesurfer> setenv TUTORIAL_DATA <path_to_tutorial_data>
You are now ready to start the Freesurfer tutorials.
FreeSurfer Tutorial Datasets - full version
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)Here is the md5sum.
- 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
fbert-feat.tgz & bert.recon.tgz - tutorial on the integration of FreeSurfer and FSL/FEAT
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:
Download using wget
The wget application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size. Mac OS NOTE: Use curl -O in place of wget.
Open a terminal, create a directory called tutorial_data where you know you have at least 100GB of space, and cd into that directory. To download, type:
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.tgz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.tar.gz &
This download will likely take several hours.
The wget application will handle poor connections, and retry if it is having problems. A failed download can be restarted by adding the -c flag to wget, which will cause it to continue from the point where a partial download stopped. Notice the commands have the ampersand, so you can run all these commands at once (although the wget output will be hard to decipher, so an alternative is to run each without the ampersand in a separate terminal). Go to the Installation section below once the files are downloaded.
Optional Verification Step
If you want to verify the files transferred correctly using md5sum, the md5sum for each of these downloads can found in files named *.md5sum.txt in this directory or get them this way:
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.md5sum.txt &
You will want to ensure that these md5sum's match what you find when you run md5sum on your own local downloads. If they do not match, the file transfer may have been faulty or there may have been a disk error. Mac OS NOTE: Use md5 -r to get the same results as md5sum. More on md5sum can be found here.
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
To setup the environment variable SUBJECTS_DIR to point to the tutorial data, type the following commands every time you open a new terminal window. Alternatively, you can include the below commands in your .cshrc or .tcshrc file so these variables are automatically set every time you open a new terminal window:
(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.).
FSL-FEAT Tutorial Data
cd $SUBJECTS_DIR tar xvfz bert.recon.tgz cd /place/for/functional/data tar xvfz fbert-feat.tgz