Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

Re: [Freesurfer] mgh conversion
by Douglas N Greve 28 Jan '13

28 Jan '13

How many vertices are on the surface? For nifti you have to reshape the size of the image so that it fits in the nifti format (requires each dim be less than 32k). If the number of vertices has a prime factor that is more than 32k, then you cannot convert it to nifti and use it in another software package (it still works in FreeSurfer, but then you could just use an mgh file then). doug On 01/28/2013 01:58 PM, Courtney Haswell wrote: > Hi, > > Was there a resolution to this thread on the FreeSurfer mail archive? > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17886.html > > I am having the same issue trying to convert a cortical thickness sig.mgh to > a NIfTI file. I want to use the statistically significant area as an ROI in > another analysis. > > Thanks, > Courtney Haswell > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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R: Re: R: R: Re: TRACULA
by stdp82＠virgilio.it 28 Jan '13

28 Jan '13

Thank you very much for you kindness Anastasia. The folder that contains .nii.gz file is correct?I'm looking the recommended trac-all update. Where can I put it? Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 28-gen-2013 16.45 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: R: Re: TRACULA Hi Stefano - The argument of the -c option is a configuration file, not a directory. For more info on trac-all and setting up the configuration file, please see the trac-all wiki page: http://www.freesurfer.net/fswiki/trac-all and tracula tutorials: http://www.freesurfer.net/fswiki/FsTutorial/Tracula a.y On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > Hi and thank you very much for your availability. > Now, I'm running tracula as following: > > trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01 > > my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used in > > previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same > that I have previously used in FSL analysis. > > Please, my questions are: > a- Are correct the command and the files (dyrectory positioning and their > extensions)? > b- Now my computer seem to running but after 1 h from the start, I visualize > on my desktop this message "Your Mac 0SX has no more space available for > application memory". > My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz > DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of 999,35 > I have download the package for (Snow)Leopard (10.5/6.x) Intel. > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 27-gen-2013 19.36 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] TRACULA > > Hi Stefano - The -prep option doesn't take an argument. Please run > trac-all with no arguments to see usage info. > > a.y > > > Hi list, > > I'm trying to run a test subject with TRACULA. > > I placed a folder in /Applications/freesurfer/subject/subject_prova which > > contains these files: data.nii.gz (DWI), bvals and bvecs (as used in > > previous FSL analysis) and T1-images.in > > /Applications/freesurfer/subject/subject_prova > > This is the command that I'm running:[iMac-di-Stefano:~] Stefano% trac-all > > -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i > > $FREESURFER_HOME/subjects/subject_prova > > ERROR: flag > > /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep > > /Applications/freesurfer/subjects/subject_prova/CON_01 --i > > /Applications/freesurfer/subjects/subject_prova > > Please, give me an help. > > > > Thanks in advance, > > > > Stefano _______________________________________________ > > 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 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] xhemi problem
by Gabriel Gonzalez Escamilla 28 Jan '13

28 Jan '13

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R: R: Re: TRACULA
by stdp82＠virgilio.it 28 Jan '13

28 Jan '13

Hi and thank you very much for your availability. Now, I'm running tracula as following: trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01 my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used in> previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same that I have previously used in FSL analysis. Please, my questions are:a- Are correct the command and the files (dyrectory positioning and their extensions)?b- Now my computer seem to running but after 1 h from the start, I visualize on my desktop this message "Your Mac 0SX has no more space available for application memory".My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of 999,35 I have download the package for (Snow)Leopard (10.5/6.x) Intel. Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 27-gen-2013 19.36 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] TRACULA Hi Stefano - The -prep option doesn't take an argument. Please run trac-all with no arguments to see usage info. a.y > Hi list, > I'm trying to run a test subject with TRACULA. > I placed a folder in /Applications/freesurfer/subject/subject_prova which > contains these files: data.nii.gz (DWI), bvals and bvecs (as used in > previous FSL analysis) and T1-images.in > /Applications/freesurfer/subject/subject_prova > This is the command that I'm running:[iMac-di-Stefano:~] Stefano% trac-all > -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i > $FREESURFER_HOME/subjects/subject_prova > ERROR: flag > /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep > /Applications/freesurfer/subjects/subject_prova/CON_01 --i > /Applications/freesurfer/subjects/subject_prova > Please, give me an help. > > Thanks in advance, > > Stefano _______________________________________________ > 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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R: Re: TRACULA
by stdp82＠virgilio.it 28 Jan '13

28 Jan '13

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TRACULA
by stdp82＠virgilio.it 27 Jan '13

27 Jan '13

Hi list, I'm trying to run a test subject with TRACULA. I placed a folder in /Applications/freesurfer/subject/subject_prova which contains these files: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.in /Applications/freesurfer/subject/subject_prova This is the command that I'm running:[iMac-di-Stefano:~] Stefano% trac-all -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i $FREESURFER_HOME/subjects/subject_prova ERROR: flag /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep /Applications/freesurfer/subjects/subject_prova/CON_01 --i /Applications/freesurfer/subjects/subject_prova Please, give me an help. Thanks in advance, Stefano

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problem with qdec in full install of 5.2 beta
by Carl Anderson 26 Jan '13

26 Jan '13

Dear Freesurfer, When trying to start qdec I get the following error: dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/qdec.bin Reason: image not found Trace/BPT trap Any suggestions for a work around? Thanks, Carl -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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mean cluster surface area in mri_glmfit
by xiangbo_2010 25 Jan '13

25 Jan '13

Dear Freesurfer Experts, I would like the mean surface area measures of each cluster i found using command line (mri_glmfit). I used mri_glmfit for a group comparison in surface area between a patient group and a healthy control group. I found 4 different significant clusters (using FDR corrected, is not Clusterwise Correction for Multiple Comparisons). I would like to extract the mean surface area of each significant cluster in the patient group and in the healthy control group. Where can i found the file with this information? thanks! Bo Xiang

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Two questions: autocorrelation correction and vertex distance
by Alex Kell 25 Jan '13

25 Jan '13

Hi Freesurfers, I have two unrelated questions. 1. I want to pre-whiten some functional data without running a GLM on them (we're going to run the GLM in matlab). It looks like fsfast does autocorrelation correction as a part of the selxavg3-sess wrapper. I tried poking around on the wiki and mailing archives, but I can't find how to pre-whiten the data without running a GLM. Is there a straightforward way? If not, I guess we could just do it in matlab. 2. Separately, we're bringing some volume masks to the surface and are preprocessing them with dilation and erosion to clean them up. We're trying to get a sense of how much is a reasonable amount to dilate and erode by, and it would be helpful to know about how far apart the adjacent surface vertices are. Roughly, what's the mean distance between adjacent vertices? Thanks in advance. Best, Alex

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Problems calling Free Surfer...
by Rosalia Dacosta Aguayo 25 Jan '13

25 Jan '13

Dear Free Surfer experts, I am having problems with my FS installation. I am working with Linux/Ubuntu version 11.10...I have followed the indications of the FS wiki and it seems that it is installed but it does not work...it does not run in the terminal and I do not know why and how can I do: osi@rosi-HP-Pavilion-dv9700-Notebook-PC:~$ cd /home/rosi/FREE_SURFER/ freesurferrosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ export FREESURFER_HOME=/home/rosi/FREE_SURFER/freesurfer rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ . $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos4-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/rosi/FREE_SURFER/freesurfer FSFAST_HOME /home/rosi/FREE_SURFER/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/rosi/FREE_SURFER/freesurfer/subjects MNI_DIR /home/rosi/FREE_SURFER/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ freesurfer FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer also refers to the structural imaging stream within the FreeSurfer suite. Users should consult the online documentation available at: https://surfer.nmr.mgh.harvard.edu Alternatively, the 'recon-all' command help-text provides adequate information to begin processing subject data, such as the sample subject 'bert' found in the 'freesurfer/subjects' directory. Type 'recon-all --help' to view this help-text. Direct comments and questions to: freesurfer(a)nmr.mgh.harvard.edu *You are running this version of FreeSurfer: freesurfer-Linux-centos4-**stable-pub-v5.1.0 rosi@rosi-HP-Pavilion-dv9700-* *Notebook-PC:~/FREE_SURFER/**freesurfer$ How can I call FreeSurfer?? *Thanks in advance, Rosalia.

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