Hi every one
Sorry for not writing subject in my previous email. If applescript was not clear in the previous email you can download it from the following page;
http://www.freesurfer.net/fswiki/Easyfreesurfer
Jamaan
On 16 July 2011 19:39, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- Re: Freesurfer Digest, Vol 89, Issue 52 (Jamaan Alghamdi)
Message: 1 Date: Sat, 16 Jul 2011 19:38:40 +0100 From: Jamaan Alghamdi jamaan.alghamdi@gmail.com Subject: Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 52 To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CAGLHyT7PGVWPqxNNXEwVAJnfiqV_H9LA13CYuMWa=PTCEBu3tA@mail.gmail.com
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Hi
Previous scripts are good but if you feel confused because you do not have that experience with scripting you can try another way;
For creating directories;
for i in 01 02 03 04 05 .....; do mkdir -p C${i}/mri/orig ; done
replace dots (.....) with numbers as much as you want and replace C with your subjects' ID
For runing mri_convert command;
for i in 01 02 03 04 05; do mri_convert C${i}.nii.gz C${i}/mri/orig/001.mgz ; done
again replace dots (.....) with numbers as much as you want and replace C with your subjects' ID
or even you can try the following applescript if you have mac system
*display dialog* "Choose your shell type" buttons {"bash", "csh or tcsh", "Cancel"} ?
with title ""
*set* diag1button *to* button returned *of* result
*if* diag1button *is* "bash" *then*
*tell* *application* "Terminal"
*set* currentTab *to* *do script* "export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh"
*end* *tell*
*else* *if* diag1button *is* "csh or tcsh" *then*
*tell* *application* "Terminal"
*set* currentTab *to* *do script* "setenv FREESURFER_HOME /Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh"
*end* *tell*
*end* *if*
*set* destination *to* (*choose folder* with prompt "Choose the destination folder")
*set* this_folder1 *to* *choose folder* with prompt "Data directory"
*set* dir *to* "mri/orig"
*tell* *application* "Finder"
*set* thePath1 *to* POSIX path *of* this_folder1
*set* mylist *to* *get* name *of* *folders* *of* this_folder1
*set* stringsList *to* mylist
*set* theChoices *to* ?
*choose from list* stringsList with prompt "You can select more than one subject's ID from the list below;
Please use mous click and Command key to highlight your selection" with title "" *with* multiple selections allowed
*set* x *to* result *as* *string*
*repeat* *with* x *in* theChoices
*set* subjectid *to* x *as* *string*
*set* ThePath3 *to* POSIX path *of* this_folder1 & subjectid
*set* t *to* (*do shell script* "ls " & quoted form *of* ThePath3)
*set* beginningToEnd *to* *text* *of* *first* *paragraph* *of* t
*set* folderName *to* x *as* *string*
*tell* *application* "Finder"
*make* *folders* *in* destination with properties {name:folderName}
*set* this_folder *to* folderName
*set* ThePath *to* POSIX path *of* destination
*set* thePath2 *to* POSIX path *of* destination & this_folder
*tell* *application* "Terminal"
*set* currentTab *to* *do script* "cd" & space & quoted form *of* thePath2 in *window* 1
*set* currentTab *to* *do script* "mkdir -p" & space & quoted form *of* dir in *window* 1
*set* currentTab *to* *do script* "mri_convert" & space & quoted form *of* ThePath3 & "/" & quoted form *of* beginningToEnd & space & quoted form *of* thePath2 & "/mri/orig/" & "001.mgz" in *window* 1
*end* *tell*
*end* *tell*
*end* *repeat*
*end* *tell*
On 16 July 2011 18:28, freesurfer-request@nmr.mgh.harvard.edu wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- Re: how can do ''mri_convert''quickly when there are too many subjects (Peter J. Molfese)
- Re : Book with FreeSurfer chapter (Simmons, Andy)
Message: 1 Date: Sat, 16 Jul 2011 12:40:27 -0400 From: "Peter J. Molfese" Peter.Molfese@yale.edu Subject: Re: [Freesurfer] how can do ''mri_convert''quickly when there are too many subjects To: freesurfer@nmr.mgh.harvard.edu Message-ID: 703DA8F6-7DD5-41A2-BD5C-0180EA4802D6@yale.edu Content-Type: text/plain; charset="us-ascii"
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:
- Save the script as fs_subject.sh
- chmod +x fs_subject.sh
- 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>
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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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