Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Problem registering labels to native space
by John Richey 18 Jul '11

18 Jul '11

Hi Doug, the .dat file that I mention below had already been converted into a fs matrix using tkregister2. -----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 12:38 PM To: John Richey Cc: 'Bruce Fischl'; 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space You can't use a flirt matrix with mri_label2label. You can convert a flirt matrix to the proper format with tkregister2 using the --fsl option (this will allow you to check the reg as well). doug John Richey wrote: > Hi Bruce, > > The labels that I have fsaverage space are 3D/volume-based and not > surface-based labels. > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Monday, July 18, 2011 12:00 PM > To: John Richey > Cc: 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: RE: [Freesurfer] Problem registering labels to native space > > Hi John > > why are you using an affine volume registration for fsaverage? Why not > use surface registration? > > Bruce > > > On Mon, 18 Jul 2011, John Richey wrote: > > >> Hi Bruce - thanks for the reply. >> >> Here is my command line: >> >> mri_label2label --srcsubject fsaverage \ --trgsubject ${SUBJECT} >> --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} \ >> --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} \ >> --regmethod volume \ --reg $SUBJECTS_DIR/$SUBJECT/mri/brain_reg.dat >> >> Where "brain_reg.dat" is the subject-specific matrix I created >> through FLIRT. However, as I mentioned, disincluding this matrix does >> not seem to change the result much. >> >> One other problem I encounter... Occasionally when I view the label >> in native space, the label itself seems to be eroded on a voxel-wise >> > basis. > >> That is, the label essentially appears as a series of non-contiguous >> dots (which if dialated would become contiguous). >> >> >> >> >> >> >> -----Original Message----- >> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Sent: Monday, July 18, 2011 11:20 AM >> To: John Richey >> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >> Subject: Re: [Freesurfer] Problem registering labels to native space >> >> Hi John >> >> can you email us your label2label cmdline? >> >> cheers >> Bruce >> >> >> On Mon, 18 Jul 2011, John Richey >> wrote: >> >> >>> 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 >>> _______________________________________________ >>> 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. >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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FreeSurfer Error during Fix Toplogy
by Kevin Liu 18 Jul '11

18 Jul '11

Hi, I'm relatively new to the FreeSurfer program and have mostly worked with processing adult brains. I am currently working on reconstructing images of young children under 5 and am consistently running into the same error for the two subjects I am running during mris_fix_topology. The error is as follows: 153 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 4 -merging segment 28 into 7 -merging segment 44 into 7 -merging segment 43 into 7 -merging segment 59 into 7 -merging segment 63 into 7 -merging segment 24 into 8 -merging segment 25 into 17 -merging segment 21 into 18 -merging segment 67 into 30 -merging segment 78 into 30 -merging segment 38 into 33 -merging segment 79 into 73 -merging segment 85 into 77 -merging segment 113 into 77 -merging segment 88 into 77 -merging segment 95 into 77 -merging segment 97 into 77 -merging segment 93 into 87 -merging segment 91 into 90 -merging segment 135 into 117 -merging segment 136 into 117 -merging segment 141 into 126 -merging segment 146 into 140 -merging segment 149 into 142 128 defects to be corrected 0 vertices coincident reading input surface /home/local/SOC/kcl388/wong_ lab/labmridata/FreeSurfer/CMH-3305/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7664 (-4.8832) -vertex loglikelihood: -7.0295 (-3.5147) -normal dot loglikelihood: -3.5134 (-3.5134) -quad curv loglikelihood: -6.0484 (-3.0242) Total Loglikelihood : -26.3577 CORRECTING DEFECT 0 (vertices=281, convex hull=141) After retessellation of defect 0, euler #=-62 (115680,331866,216124) : difference with theory (-125) = -63 CORRECTING DEFECT 1 (vertices=100, convex hull=64) After retessellation of defect 1, euler #=-61 (115689,331920,216170) : difference with theory (-124) = -63 CORRECTING DEFECT 2 (vertices=12, convex hull=20) After retessellation of defect 2, euler #=-60 (115690,331929,216179) : difference with theory (-123) = -63 CORRECTING DEFECT 3 (vertices=395, convex hull=187) After retessellation of defect 3, euler #=-59 (115735,332152,216358) : difference with theory (-122) = -63 CORRECTING DEFECT 4 (vertices=7865, convex hull=2299) The defects never completely correct, and the program just hangs on correcting one of the defects (in this case 'DEFECT 4'). Do you have any suggestions as to where to go from here? I have checked talairach and done skull stripping edits, none of which seemed to have worked. Best, Kevin -- Kevin Liu MD Candidate 2014 Feinberg School of Medicine -- Kevin Liu MD Candidate 2014 Feinberg School of Medicine

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Re: [Freesurfer] Problem registering labels to native space
by John Richey 18 Jul '11

18 Jul '11

Hi Bruce, The labels that I have fsaverage space are 3D/volume-based and not surface-based labels. -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 12:00 PM To: John Richey Cc: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] Problem registering labels to native space Hi John why are you using an affine volume registration for fsaverage? Why not use surface registration? Bruce On Mon, 18 Jul 2011, John Richey wrote: > Hi Bruce - thanks for the reply. > > Here is my command line: > > mri_label2label --srcsubject fsaverage \ --trgsubject ${SUBJECT} > --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} \ > --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} \ > --regmethod volume \ --reg $SUBJECTS_DIR/$SUBJECT/mri/brain_reg.dat > > Where "brain_reg.dat" is the subject-specific matrix I created through > FLIRT. However, as I mentioned, disincluding this matrix does not seem > to change the result much. > > One other problem I encounter... Occasionally when I view the label > in native space, the label itself seems to be eroded on a voxel-wise basis. > That is, the label essentially appears as a series of non-contiguous > dots (which if dialated would become contiguous). > > > > > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Monday, July 18, 2011 11:20 AM > To: John Richey > Cc: 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: Re: [Freesurfer] Problem registering labels to native space > > Hi John > > can you email us your label2label cmdline? > > cheers > Bruce > > > On Mon, 18 Jul 2011, John Richey > wrote: > >> 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 >> _______________________________________________ >> 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] Problem registering labels to native space
by John Richey 18 Jul '11

18 Jul '11

Hi Bruce - thanks for the reply. Here is my command line: mri_label2label --srcsubject fsaverage \ --trgsubject ${SUBJECT} --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} \ --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} \ --regmethod volume \ --reg $SUBJECTS_DIR/$SUBJECT/mri/brain_reg.dat Where "brain_reg.dat" is the subject-specific matrix I created through FLIRT. However, as I mentioned, disincluding this matrix does not seem to change the result much. One other problem I encounter... Occasionally when I view the label in native space, the label itself seems to be eroded on a voxel-wise basis. That is, the label essentially appears as a series of non-contiguous dots (which if dialated would become contiguous). -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 11:20 AM To: John Richey Cc: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space Hi John can you email us your label2label cmdline? cheers Bruce On Mon, 18 Jul 2011, John Richey wrote: > 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 > _______________________________________________ > 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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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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