Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Problem registering labels to native space
by John Richey 18 Jul '11

18 Jul '11

Dear freesurfer experts, I have a series of labels corresponding to clusters of significant activation in fsaverage space. I want to map these back to native space using mri_label2label, however when I view the individual (native) labels, the registration is way off and the labels do not map into plausible space. I have tried using talairach space as an intemediary (by omitting the --reg flag in mri_label2label), as well as using fsl tools (FLIRT) to create a registration matrix but unfortunately I cannot seem to get the label into the right space to query my ces maps in funcroi-sess. Have others encountered this problem? And how might I create a more robust registration between fsaverage and native space to facilitate the spatial transformation of my labels? Thanks very much in advance, John

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Registering Cortical Thickness Values on average subject
by matthias 17 Jul '11

17 Jul '11

Hello everybody, I ran the recon_all routine on a number of images of the ADNI database. The goal is to extract first of all the cortical thickness values. In order to compare the values in a classification process, eg. Alzheimer vs Normal I want to register all images to a template subject. Does anybody know how to achieve this? Thanks in advance, Matthias Schlögl

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Re : Book with FreeSurfer chapter
by Simmons, Andy 16 Jul '11

16 Jul '11

There are also several other chapters of the same book using Freesurfer in AD, including Magnetic Resonance Imaging and Magnetic Resonance Spectroscopy for Detection of Early Alzheimer's Disease / Eric Westman, Lars-Olof Wahlund, Catherine Foy, Michaela Poppe, Allison Cooper, Declan Murphy, Christian Spenger, Simon Lovestone and Andrew Simmons Combinatorial Markers of Mild Cognitive Impairment Conversion to Alzheimer's Disease - Cytokines and MRI Measures Together Predict Disease Progression / Simon J. Furney, Deborah Kronenberg, Andrew Simmons, Andreas Güntert, Richard J. Dobson, Petroula Proitsi, Lars-Olof Wahlund, Iwona Kloszewska, Patrizia Mecocci, Hilkka Soininen, Magda Tsolaki, Bruno Vellas, Christian Spenger and Simon Lovestone Best wishes, Andy Simmons ----- Date: Fri, 15 Jul 2011 20:36:01 -0300 From: Pedro Paulo de Magalh?es Oliveira Junior <ppj(a)netfilter.com.br> Subject: [Freesurfer] Book with FreeSurfer chapter To: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAPSXCjqtiYDJMAFvxGWu=k9NuTE8zf1JdOAwMv3HSBiuAwQhSQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Just for information: *Handbook of Imaging the Alzheimer Brain* * Editors: J.W. Ashford, A. Rosen, M. Adamson, P. Bayley, O. Sabri, A. Furst, S.E. Black and M. Weiner July 2011, 824 pp., hardcover ISBN 978-1-60750-792-5 (print) ** The chapter that describes the usage of FreeSurfer in AD is "Automated Volumetric Methods to Detect Alzheimer's Disease" / Pedro Paulo de Magalh?es Oliveira Jr. et al. * ---- Dr Andy Simmons Reader in Neuroimaging & Consultant Clinical Scientist Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre Institute of Psychiatry, Box P089 Kings College London De Crespigny Park London, SE5 8AF, UK Email - andy.simmons(a)kcl.ac.uk Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338 Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-… ResearcherID - http://www.researcherid.com/rid/B-8848-2008 Fax +44 (0)203 228 2116 [cid:image001.png@01CC43EE.317991F0]<http://msc-neuroimaging.com/>

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Re: [Freesurfer] how can do ''mri_convert''quickly when there (applescript)
by Jamaan Alghamdi 16 Jul '11

16 Jul '11

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(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)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: > > 1. 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(a)gmail.com> > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 52 > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAGLHyT7PGVWPqxNNXEwVAJnfiqV_H9LA13CYuMWa=PTCEBu3tA(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > 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(a)nmr.mgh.harvard.edu> wrote: > > > Send Freesurfer mailing list submissions to > > freesurfer(a)nmr.mgh.harvard.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > or, via email, send a message with subject or body 'help' to > > freesurfer-request(a)nmr.mgh.harvard.edu > > > > You can reach the person managing the list at > > freesurfer-owner(a)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: > > > > 1. Re: how can do ''mri_convert''quickly when there are too many > > subjects (Peter J. Molfese) > > 2. Re : Book with FreeSurfer chapter (Simmons, Andy) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sat, 16 Jul 2011 12:40:27 -0400 > > From: "Peter J. Molfese" <Peter.Molfese(a)yale.edu> > > Subject: Re: [Freesurfer] how can do ''mri_convert''quickly when there > > are too many subjects > > To: freesurfer(a)nmr.mgh.harvard.edu > > Message-ID: <703DA8F6-7DD5-41A2-BD5C-0180EA4802D6(a)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: > > 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(a)jonca.org> > > > Subject: Re: [Freesurfer] how can do ''mri_convert''quickly when there > > > are too many subjects > > > To: ??? <wgh0805(a)126.com> > > > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > > > Message-ID: > > > < > > CABphhh-ZcMapCqq+0x66d0EXqQgdt-vPVojXt30O0P63kzoLAw(a)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(a)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 > > >> > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer(a)nmr.mgh.harvard.edu > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> > > >> The information in this e-mail is intended only for the person to whom > > it is > > >> addressed. If you believe this e-mail was sent to you in error and the > > >> e-mail > > >> contains patient information, please contact the Partners Compliance > > >> HelpLine at > > >> http://www.partners.org/complianceline . If the e-mail was sent to > you > > in > > >> error > > >> but does not contain patient information, please contact the sender > and > > >> properly > > >> dispose of the e-mail. > > >> > > >> > >

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Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 52
by Jamaan Alghamdi 16 Jul '11

16 Jul '11

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(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)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: > > 1. Re: how can do ''mri_convert''quickly when there are too many > subjects (Peter J. Molfese) > 2. Re : Book with FreeSurfer chapter (Simmons, Andy) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 16 Jul 2011 12:40:27 -0400 > From: "Peter J. Molfese" <Peter.Molfese(a)yale.edu> > Subject: Re: [Freesurfer] how can do ''mri_convert''quickly when there > are too many subjects > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <703DA8F6-7DD5-41A2-BD5C-0180EA4802D6(a)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: > 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(a)jonca.org> > > Subject: Re: [Freesurfer] how can do ''mri_convert''quickly when there > > are too many subjects > > To: ??? <wgh0805(a)126.com> > > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > > Message-ID: > > < > CABphhh-ZcMapCqq+0x66d0EXqQgdt-vPVojXt30O0P63kzoLAw(a)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(a)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 > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> The information in this e-mail is intended only for the person to whom > it is > >> addressed. If you believe this e-mail was sent to you in error and the > >> e-mail > >> contains patient information, please contact the Partners Compliance > >> HelpLine at > >> http://www.partners.org/complianceline . If the e-mail was sent to you > in > >> error > >> but does not contain patient information, please contact the sender and > >> properly > >> dispose of the e-mail. > >> > >> >

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Re: [Freesurfer] how can do ''mri_convert''quickly when there are too many subjects
by Peter J. Molfese 16 Jul '11

16 Jul '11

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(a)jonca.org> > Subject: Re: [Freesurfer] how can do ''mri_convert''quickly when there > are too many subjects > To: ??? <wgh0805(a)126.com> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CABphhh-ZcMapCqq+0x66d0EXqQgdt-vPVojXt30O0P63kzoLAw(a)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(a)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 >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >>

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Book with FreeSurfer chapter
by Pedro Paulo de Magalhães Oliveira Junior 15 Jul '11

15 Jul '11

Just for information: *Handbook of Imaging the Alzheimer Brain* * Editors: J.W. Ashford, A. Rosen, M. Adamson, P. Bayley, O. Sabri, A. Furst, S.E. Black and M. Weiner July 2011, 824 pp., hardcover ISBN 978-1-60750-792-5 (print) ** The chapter that describes the usage of FreeSurfer in AD is "Automated Volumetric Methods to Detect Alzheimer's Disease" / Pedro Paulo de Magalhães Oliveira Jr. et al. *

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how can do ''mri_convert''quickly when there are too many subjects
by 汪贵宏 15 Jul '11

15 Jul '11

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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help on MAC ".licence" file
by 119829640 15 Jul '11

15 Jul '11

Hi: To register the freesurfer, I use the command "gedit .licence" and paste my registration information to it in ubuntu. It does works. However, I got a trouble when using MAC laptop. I don't know how to create the .licence file. I have got the registration information for MAC. I will be very appreciated if you can give me some clues and answers. Thank u very much.

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Re: [Freesurfer] DOF and smoothing in mri_glmfit
by Agnieszka Burzynska 15 Jul '11

15 Jul '11

Dear Doug, I wanted to follow up on our discussion: I have re-run the analysis with the smoothing during the 1st level analysis and indeed the activation pattern looks more as we expect from the 3D analysis in FSL, although the regions that are "active" are the same. Thank you for your advice! Best, Aga On 7/7/11 5:14 PM, "Agnieszka Burzynska" <burzynska(a)mpib-berlin.mpg.de> wrote: > Thank you! I think I will just try it out: now run it as it is but also run > the 1st level with smoothing, as I need to add some contrasts anyway. Then I > should also know the difference between volume and surface smoothing. > Cheers, > Aga > > On 7/7/11 5:07 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > >> The problem with doing the smoothing at the first level in FEAT is that >> it will be volume-based, not surface-based. I'm not sure what to tell >> you about using the varcopes. They will certainly be very noisy without >> smoothing, so probably smoothing is a good idea, even if it's volume-based. >> >> doug >> >> Agnieszka Burzynska wrote: >>> Dear Doug, >>> Thank you so much. I completely see you point, but I have re-run the 1st >>> level feat without smoothing just because it has been recommended not to >>> smooth in the volume and then transfer it onto the surface, but rather first >>> smooth on the surface >>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer) >>> >>> What I plan to do in the end is to include the cortical thickness as the >>> vertex-wise covariate in the functional group analysis. >>> >>> So the final analysis will be on the group level, where, as you say, the >>> varcopes should not matter that much. >>> >>> However, I was also thinking of analyzing varcopes in addition to copes >>> (group analysis) to relate the variance of BOLD signal to the thickness. >>> >>> Would you then recommend going back and taking the initial 1st level >>> analysis with regular smoothing? >>> >>> Thank you! >>> Aga >>> >>> On 7/7/11 4:43 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: >>> >>> >>>> Hi Aga, your commands look right. For the DOF, it should be the sum of >>>> the DOFs from all the runs (probably won't make much of a difference). >>>> Smoothing is a bit of an issue when you want to look at individual >>>> results. Technically, you should smooth before you do the first level >>>> analysis (ie, before your compute the varcope), but this would require >>>> doing the FEAT analysis directly on surface data. Smoothing after >>>> computing the varcope means that the varcope will not be accurate (it >>>> will be too large). The penalty is that you will see less activation >>>> than you should. At the group level, this is not such a big deal because >>>> you're either not using the varcope or you are using it as a weight. >>>> doug >>>> >>>> Agnieszka Burzynska wrote: >>>> >>>>> Dear all, >>>>> I am combining 3 runs of a subject using fixed effects GLM and I wanted to >>>>> make sure I am doing the right thing. >>>>> >>>>> For each subject I use: >>>>> mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof >>>>> 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label >>>>> $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5 >>>>> >>>>> , while lh.cope1.mgh contains the concatenated cope1 images of the same >>>>> subject in fsaverage space (the same for varcope1). >>>>> >>>>> 1) Is it the right way? >>>>> 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it >>>>> correct? >>>>> 3) The functional data has not been smoothed in the 1st level analysis in >>>>> FSL (as recommended), and also not smoothed during sampling the copes to a >>>>> common space. Therefore I want to smooth it here for the first time, but >>>>> only with 5mm. Does it sound right? >>>>> >>>>> Cheers, >>>>> Aga >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>>> >>> >>> >>>

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