Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

converting a volume to a surface
by Aaron Tanenbaum 10 Jul '13

10 Jul '13

Hola Freesurfers, I am new to Freesurfer and still learning the basics. I have been given a project and have not found a way to do it. Part of this task involves taking a 4dfp volume time series and convert it to a time series of a surface. This 4dfp I have is a statistical analysis mapped on to a specific atlas volume. Does anyone know of a way to do this. Any help will be highly appreciated. Gracias Aaron Tanenbaum

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Recon-all command not found
by Stéphane Poulin 10 Jul '13

10 Jul '13

Hello Freesurfer experts I have just installed Freesurfer and tried to run recon-all command. I get these "command not found" errors. Any idea? Stephane Last login: Wed Jul 10 21:42:55 on ttys001 [silicium:~] stephanep% cd /Volumes/Macintosh_HD_Donnees/Applications/ [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% setenv FREESURFER_HOME freesurfer [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME freesurfer FSFAST_HOME freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR freesurfer/subjects MNI_DIR freesurfer/mni [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% setenv SUBJECTS_DIR /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/ [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% recon-all -i /Volumes/Macintosh_HD_Donnees/Imaging/ADNI_2/002_S_4171/MPRAGE/2011-08-08_17_22_19.0/S118013/ADNI_002_S_4171_MR_MPRAGE_br_raw_20110809145237100_127_S118013_I249535.dcm -subjid 002_S_4171 Subject Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects Actual FREESURFER_HOME /Volumes/Macintosh_HD_Donnees/Applications/freesurfer Darwin silicium.crulrg.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 mri_motion_correct.fsl: Command not found. talairach_avi: Command not found. tkregister2_cmdl: Command not found. nu_correct: Command not found. mri_make_uchar: Command not found. mri_normalize: Command not found. mri_watershed: Command not found. mri_gcut: Command not found. mri_segment: Command not found. mri_label2label: Command not found. mri_em_register: Command not found. mri_ca_normalize: Command not found. mri_ca_register: Command not found. mri_ca_label: Command not found. mri_pretess: Command not found. mri_fill: Command not found. mri_tessellate: Command not found. mri_concatenate_lta: Command not found. mri_normalize_tp2: Command not found. mris_smooth: Command not found. mris_inflate: Command not found. mris_curvature: Command not found. mris_sphere: Command not found. mris_fix_topology: Command not found. mris_topo_fixer: Command not found. mris_ca_label: Command not found. mris_euler_number: Command not found. mris_make_surfaces: Command not found. mris_register: Command not found. mris_volmask: Command not found. mris_anatomical_stats: Command not found. mrisp_paint: Command not found. mris_curvature_stats: Command not found. mris_calc: Command not found. mri_robust_register: Command not found. mri_robust_template: Command not found. mri_and: Command not found. mri_or: Command not found. mri_fuse_segmentations: Command not found. mri_segstats: Command not found. cp: freesurfer/bin/recon-all: No such file or directory /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/002_S_4171 \n mri_convert /Volumes/Macintosh_HD_Donnees/Imaging/ADNI_2/002_S_4171/MPRAGE/2011-08-08_17_22_19.0/S118013/ADNI_002_S_4171_MR_MPRAGE_br_raw_20110809145237100_127_S118013_I249535.dcm /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/002_S_4171/mri/orig/001.mgz \n mri_convert: Command not found. Darwin silicium.crulrg.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 recon-all -s 002_S_4171 exited with ERRORS at Wed Jul 10 21:53:13 EDT 2013 For more details, see the log file /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/002_S_4171/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep%

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Re: [Freesurfer] application of mri_cvs_register question
by Hoptman, Matthew 10 Jul '13

10 Jul '13

Hi Lilla, Unfortunately, when I run: mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z ../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o diffvol2CVS.nii.gz --no-save-reg I now get: Using the m3z file as it is; no assumed location. regio_read_register(): Success Error reading R[3][0] from diff2anat.bbr.mat Matrix from regfile: -0.001 0.972 -0.234 -3.311; -0.001 0.234 0.972 69.949; 0.000 0.000 0.000 1.000; 0.000 0.000 0.000 0.000; Best, Matt -----Original Message----- From: Lilla Zollei [mailto:lzollei@nmr.mgh.harvard.edu] Sent: Wednesday, July 10, 2013 6:07 PM To: Hoptman, Matthew Subject: RE: [Freesurfer] application of mri_cvs_register question Hi Matt, As diff2anat.bbr.mat was created by bbregister, I believe you should be able to use --reg diff2anat.bbr.mat in your command. Let me know if you encounter further problems. Lilla On Wed, 10 Jul 2013, Hoptman, Matthew wrote: > Hi Lilla, > I want to apply the transform to both the dtifit_FA and tracula tracts to put them into cvs space (given the m3z file, as well). The goal is to get "average" tracts across my subjects. The relevant transforms I have in my dmri/xfms would seem to be: > diff2anat.bbr.mat > diff2anatorig.bbr.mat > diff2mni.bbr.mat > > Thanks, > Matt > -----Original Message----- > From: Lilla Zollei [mailto:lzollei@nmr.mgh.harvard.edu] > Sent: Tuesday, July 09, 2013 8:01 PM > To: Hoptman, Matthew > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] application of mri_cvs_register question > > > Hi, > > What type of registration file do you have representing the diff2anat > transformation? With mri_vol2vol you can use many different types of > transformations, if you switch the --reg flag to --xfm, --fsl or --lta, > for example. > > Lilla > > On Mon, 8 Jul 2013, Hoptman, Matthew wrote: > >> >> Hi all, >> >> I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on how to do so to DTI data processed in Tracula. The command in the “Multimodal integration and inter-subject registration” tutorial is: >> >> mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg >> >> >> >> But in Tracula, there are no “register.dat” files, or indeed no *.dat files. Is there a way to convert one of the *.mat files in the dmri/xfms directory to a *.dat file? Also, given that I think Tracula and dt_recon use different transformation algorithms, which Tracula >> transform should I choose? >> >> >> >> Thanks, >> >> Matt >> >> >> >> Matthew J. Hoptman, PhD >> Research Scientist V >> Nathan S. Kline Institute for Psychiatric Research >> >> Research Associate Professor in Psychiatry >> NYU School of Medicine >> >> >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this >> e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. >> >> PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >> >> >> >> ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ >> Conserve Resources. Print only when necessary. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you >> are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, >> you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >> > > > 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. > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

2 1

Discrepancy between surface data of Heschl's gyrus and its image
by Klein, Holger 10 Jul '13

10 Jul '13

Dear Freesurfers, I averaged 42 subjects with make_average_subject focusing on Heschl's Gyrus and finally got the image attached (for both atlases (Desikan = Atlas I, Destrieux = Atlas II). Gray matter surface calculations for Heschl's gyrus showed the following mean values (in mm^2): Atlas I lh = 439 (SD 60), rh = 323 (SD 46) Atlas II lh = 340 (SD 70), rh = 253 (SD 47) Heschl's gyrus depicted in the attached image looks considerably larger for Atlas II, but the surface analysis gives me smaller values for mean surface calculation (Atlas II < Atlas I) How can that be explained? Thanks in advance Holger

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Freesurfer stats into REDCap
by Scott Burns 10 Jul '13

10 Jul '13

Hey all, I want to announce a little tool I've been working on. I wanted to be able to put Freesurfer stats into our REDCap databases so our group can more easily analyze these measures against behavioral data. I wrote a tiny little python package that you can find at github.com/sburns/recon-stats to do just that. Hope at least someone else out there can find this useful! Scott Burns Sr. Research Imaging Specialist Education and Brain Science Research Laboratory Vanderbilt University Nashville, TN

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Fwd: wm surf error
by Jason Tourville 10 Jul '13

10 Jul '13

Hello freesurfers, In the attached pic, the red cross hairs fall in the calcarine fissure (right hemisphere). In this scan (and some others I've reviewed recently), this cortex falls within the wm surface and is therefore excluded from the cortical surface. This is despite that area not being labeled as white matter in the wm.mgz volume. It's also despite my efforts to creatively erase wm volume voxels to encourage the wm surface to exclude these cortical voxels. Is there a fix for this type of error? The data were generated with FS v5.3. No control points were set. Thanks for any help, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755 -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

2 1

(no subject)
by Shani Ben Amitay 10 Jul '13

10 Jul '13

Hello freesurfers I'm trying to reconstruct the pial and white surfaces of the rat. The input image is an inverted T2 (attached) and the segmentation to white and gray matter is done using an in house tool. using the following I'm trying to extract the surfaces: mri_fill -CV 120 128 89 -PV 124 137 111 -PV 123 133 113 -PV 123 136 110 -PV123 134 117 mri/white.mgz mri/filled/filled.mgz mri_pretess mri/filled/filled.mgz 255 mri/brain.mgz mri/filled-pretess255. mgz mri_tessellate mri/filled-pretess255.mgz 255 surf/lh.orig.nofix mris_extract_main_component surf/lh.orig.nofix surf/lh.orig.nofix mris_smooth -nw surf/lh.orig.nofix surf/lh.smoothwm.nofix mris_inflate -no-save-sulc surf/lh.smoothwm.nofix surf/lh.inflated.nofix mris_make_surfaces -noaparc -noaseg -mgz -T1 brain ratT1 lh -pial the white surface(red) is ok, the pial surface(yellow) not at all. Any idea if it's possible to fix it? is it possible to give the gray matter segmentation as an initial guess? Thanks ! Shani

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limited number of variables in qdec.table.dat?
by Mürner-Lavanchy, Ines 10 Jul '13

10 Jul '13

Dear experts, is there a limitation concerning the number of variables in qdec (in qdec.table.dat)? I obtained different results when I included about 30 variables vs. only 10 variables in qdec.table.dat for exactly the same analysis, involving only 2 of the variables (I did not include the other variables as nuisance or covariates). I thought there was no influence of the variables I choose for qdec.table.dat, as long as I don't include them in the analysis in qdec. I suppose I'm wrong there? Thank you very much for your help, Ines

2 1

Fwd: how to use mris_register?
by fatma zribi 10 Jul '13

10 Jul '13

---------- Forwarded message ---------- From: fatma zribi <zribi.fatma(a)gmail.com> Date: 2013/7/10 Subject: Re: [Freesurfer] how to use mris_register? To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi Bruce, Thank you very much for your help but it still don't work. mris_register s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere avg_all_subjects_SD/lh.reg.template.tif lh.sphere_reg $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere... MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere): could not open file No such file or directory mris_register: could not read surface file s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere No such file or directory note that the file exist in the folder and i have changed the SUBJECT_DIR to the appropriate folder Thank you very much for your help with best regards, Fatma 2013/7/9 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Fatma > > don't use the -1 flag if you are regtering to a template, only if you are > registering individual surfaces to each other. You probably want the output > to be named lh.sphere_reg and go in the s000/surf dir. > > cheers > Bruce > > > On Tue, 9 Jul 2013, fatma zribi wrote: > > Dear Mr, >> >> When I execute mris_register to register one subject to a template., I >> have this message of error: >> >> mris_register -1 s000/surf/lh.sphere avg_all_subjects_SD/lh.reg.**template.tif >> sphere_reg >> treating target as a single subject's surface... >> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ >> reading surface from s000_open_brain_sanlm_+TIR_** >> normlalized/surf/lh.sphere... >> MRISread(s000_open_brain_**sanlm_+TIR_normlalized/surf/**lh.sphere): >> could not open file >> No such file or directory >> mris_register: could not read surface file s000/surf/lh.sphere >> No such file or directory >> >> note that the file exist in the specifeid SUBJECT_DIR >> >> Thank you for your help >> >> Fatma >> >> >> >> > > 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<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. >

3 4

Error after recon_all on pre-BETed image
by Lin, Richard Lee-Tsong 10 Jul '13

10 Jul '13

Hi FS gurus, For whatever reason, BET worked better on my structural image than mri_watershed, so I used a BET image with recon-all -autorecon1 -noskullstrip. Here is a summary of the codes that I used: bet structural.nii structural_brain.nii.gz recon-all -i structural.nii -s {subjid} recon-all -autorecon1 -noskullstrip -s {subjid} mri_convert structural_brain.nii.gz {FS_directory}/{subjid}/mri/brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid {subjid} Stage 1 ran without errors. Stage 2 ran with errors, but when I checked the log (see attached), and the only message that resembled error to me was the following: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH Is there something I did wrong? Thanks. Best, Richard

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