A script is definitely the easiest way to process quite a few subjects. You can save some headache by using a recon-all command with an input for your image files. For example: "recon-all -s sleep_001 -i sleep_001.nii -all" will create a subject folder in the correct location named sleep_001 and begin the entire freesurfer pipeline taking the NIFTI image sleep_001.nii as the input. You can modify it to just import the files by dropping the "-all".

I've included a bash script below for simplifying this. This script takes the NIFTI files you want to process as arguments and then automatically sets the Subject ID and begins processing. Once it completes a single subject, it will start the next subject. You can track the progress of subjects by seeing which folders have been created in the SUBJECTS_DIR. If you have a multiprocessor system, you can run the script with different subjects in multiple terminal windows.

To execute the script: 1. Save the script as fs_subject.sh 2. chmod +x fs_subject.sh 3. place the script in a folder with all of your NIFTI files (not required but may make your life easier) 4. execute the script with ./fs_subject.sh sleep_001.nii sleep_002.nii sleep_003.nii (don't forget to replace sleep_* with your NIFTI file names) 4a. If your subjects meet a standard naming convention you could do something like: ./fs_subject.sh sleep_*.nii (this would submit all subjects fitting the pattern of having "sleep_" at the beginning of the name.

#!/bin/bash # ./fs_subject.sh # takes nifti files as arguments for submitting into freesurfer pipeline

#setup Freesurfer if not currently loaded on path export FREESURFER_HOME=/usr/local/freesurfer #source $FREESURFER_HOME/SetUpFreeSurfer.sh . $FREESURFER_HOME/SetUpFreeSurfer.sh

for FS in $* do subjectID=$(/bin/echo $FS | /usr/bin/sed 's/.nii//') recon-all -s $subjectID -i $FS -all done

Hope this helps! Ultimately if you have a lot of computers and a lot of subjects, using Sun Grid Engine (SGE) or Apple's xgrid (if you have Macs) can really expedite the processing of subjects.

Best, Peter

Date: Fri, 15 Jul 2011 12:22:38 -0500 From: Freesurfer Local Archive freesurfer@jonca.org Subject: Re: [Freesurfer] how can do ''mri_convert''quickly when there are too many subjects To: ??? wgh0805@126.com Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Message-ID: CABphhh-ZcMapCqq+0x66d0EXqQgdt-vPVojXt30O0P63kzoLAw@mail.gmail.com Content-Type: text/plain; charset=UTF-8

I suspect that your subject directory/file names will match some pattern. You can use combination of a loop and shell "ls" command to cycle through all the subjects matching provided pattern. For example if you have data in directories you would do something line this:

#!/bin/tcsh

cd /path/to/native/files

for x in `ls -dA1 name_pattern_*`; do mkdir -p $SUBJECTS_DIR/${x}/mri/orig $FREESURFER_HOME/bin/mri_convert ${x}.nii.gz $SUBJECTS_DIR/${x}/mri/orig/001.mgz done

If all files are in the same directory substitute '-dA1' for "-A1" and it should work. Note this assumes that you have nifti files, for DICOM you will need to modify it further.

Cheers,

Jacek

2011/7/15 ??? wgh0805@126.com:

...

??Hi Bruce,

?????In our research,if there are?100 subjects,how?can I ?process these data easily.For example?when I want to compare their thickness's difference?at first?I should do " mri_convert? bert.nii bert.nii.gz",but when there are too many subjects,is there a way to do all of these 100 subjects at the same time?

?Many thanks, ?Wang

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