Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

aparc2aseg error
by Derin Cobia 12 Jun '07

12 Jun '07

I'm getting the following error on several of my subjects during the aparc2aseg stage: _________________________ #@# AParc-to-ASeg Sat Jun 9 12:19:58 EDT 2007 /disk/eli/freesurfer/conte_flash/5111 mri_aparc2aseg --s 5111 --ribbon SUBJECTS_DIR /disk/eli/freesurfer/conte_flash subject 5111 outvol /disk/eli/freesurfer/conte_flash/5111/mri/aparc+aseg.mgz useribbon 1 baseoffset 0 Reading lh white surface /disk/eli/freesurfer/conte_flash/5111/surf/lh.white Building hash of lh white Reading lh pial surface /disk/eli/freesurfer/conte_flash/5111/surf/lh.pial Building hash of lh pial ERROR: lh white and pial have a different number of vertices (190233,189041) Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jun 9 12:20:07 EDT 2007 _______________________________ Do I need to reprocess from a certain stage on, or redo the whole thing? What would have caused this (it didn't happen with some other subjects during the same process batch). I couldn't find any info on this in the archive or wiki, I'm running 3.0.4. Thanks, Derin

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changing subject's name
by Woo Suk, Tae 12 Jun '07

12 Jun '07

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } After recon-all -s tfe10 (subject name) -all, I changed a subject's name (tfe10) to 001.when I performed group analysis (mris_make_average_surface), I had the error massage.How can I correct it?---------------------------------------------------------------------------------------------------------------#@# processing subject 1/42 001... Reading /usr/local/freesurfer/subjects/001/surf/rh.sphere.reg Talairach transform /usr/local/freesurfer/subjects/tfe10/mri/transforms/talairach.xfm does not exist ...Loading tal xfm file /usr/local/freesurfer/subjects/001/mri/transforms/talairach.xfm Read /usr/local/freesurfer/subjects/001/mri/T1.mgz Surface area: 872.5 cm^2 Applying linear transform Talairach transform /usr/local/freesurfer/subjects/tfe10/mri/transforms/talairach.xfm does not exist ...Loading tal xfm file /usr/local/freesurfer/subjects/001/mri/transforms/talairach.xfm--------------------------------------------------------------------------------------------------------------------Woo Suk, Tae

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Manually editing brainmask.mgz
by Jared Conley 11 Jun '07

11 Jun '07

FreeSurfer community, I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command <tkmedit subjid brainmask.mgz> and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas? Thanks, Jared

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reg -feat2anat error reg -feat2anat error
by Furlong, Carolyn 11 Jun '07

11 Jun '07

Hi Doug we tried adding the binaries Doug sent us (MRI_convert, reg2anat and tkregister2, make average subject, make average surface anfd make avergae volume), but now we get a different error:reg-feat2anat --feat ./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. What should I do? Best wishes Carolyn -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 21/05/2007 17:16 To: Furlong, Carolyn Cc: Freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] reg -feat2anat error Did you see my email from last week? It looks like the problem was fixed with new versions of a few programs. doug Furlong, Carolyn wrote: > > Hi Doug > > Please find attached the logfile that you requested, sorry for the > delay, I am only able to work on this one day a week. > > Best wishes > Carolyn > > > > > > Actually, I wanted the log file found in > featdir/reg/freesurfer/reg-feat2anat.log. > > doug > > Furlong, Carolyn wrote: > > > Hi > > > > > > niiRead(): unsupported timing pattern in > Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz > > > > sorry for the delay, > > > > Best wishes > > > > Carolyn > > > > can you send the log file? > > > > Furlong, Carolyn wrote: > > > >> Hi, > >> > >> When I try to register my functional data to anatomical data using > >> > >> reg-feat2anat --feat feat_directory --subject subject_name > >> > >> I get the following error message > >> > >> ERROR: could not read ///example_func.nii.gz as 24 > >> > >> What does this mean? And how can I fix this? > >> > >> Best wishes > >> Carolyn > >> > >> > >>_______________________________________________ > >>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 > > > >In order to help us help you, please follow the steps in: > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > >_______________________________________________ > >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 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >------------------------------------------------------------------------ > >Mon May 21 10:38:18 BST 2007 >/disc2/Kate/Flatmap1 >/home/progs/freesurfer/bin//reg-feat2anat >--feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore >Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 i686 i686 i386 GNU/Linux >mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz >mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz >reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz... >TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >i_ras = (-1, 0, 0) >j_ras = (0, 0, -1) >k_ras = (0, 1, 0) >writing to /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz... >example_func ras_good_flag >------------------------------------------------------- >Initializing exf2anat from crude std2anat >tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader --noedit >target volume /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz >movable volume /home/progs/fsl/etc/standard/avg152T1_brain.img >reg file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat >LoadVol 0 >$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ >Diagnostic Level -1 >INFO: loading target /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz >Ttarg: -------------------- >-1.000 0.000 0.000 128.000; > 0.000 0.000 1.000 -128.000; > 0.000 -1.000 0.000 128.000; > 0.000 0.000 0.000 1.000; >INFO: loading movable /home/progs/fsl/etc/standard/avg152T1_brain.img >Tmov: -------------------- >-2.000 0.000 0.000 91.000; > 0.000 0.000 2.000 -91.000; > 0.000 -2.000 0.000 109.000; > 0.000 0.000 0.000 1.000; >mkheaderreg = 1, float2int = 0 >---- Input registration matrix (computed) -------- > 1.000 0.000 0.000 0.000; > 0.000 0.000 1.000 30.861; > 0.000 -1.000 0.000 -52.627; > 0.000 0.000 0.000 1.000; >--------------------------------------- >---- Input registration matrix -------- > 1.000 0.000 0.000 0.000; > 0.000 0.000 1.000 30.861; > 0.000 -1.000 0.000 -52.627; > 0.000 0.000 0.000 1.000; >subject = subject-unknown >RegMat --------------------------- > 1.000 0.000 0.000 0.000; > 0.000 0.000 1.000 30.861; > 0.000 -1.000 0.000 -52.627; > 0.000 0.000 0.000 1.000; >register: file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat written >FSLOUTPUTTYPE NIFTI_GZ >tkreg2FSL: mov det = -8, ref det = -1 >mri_matrix_multiply -fsl -bin -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat -om /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat >betfunc /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet >Mon May 21 10:38:32 BST 2007 >flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii.gz -init /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 >------------------------------------------------------- >tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat --fslreg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat --noedit --mgz >niiRead(): unsupported timing pattern in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz >---- FSL registration matrix -------- > 0.974 0.200 0.103 12.477; >-0.093 -0.059 0.994 75.631; > 0.205 -0.978 -0.039 180.824; > 0.000 0.000 0.000 1.000; >--------------------------------------- >INFO: no target volume specified, assuming FreeSurfer orig volume. >target volume orig >movable volume /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz >reg file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat >LoadVol 0 >$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ >Diagnostic Level -1 >ERROR: could not read /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz as 24 >ERROR: tkregister2 > > >------------------------------------------------------------------------ > >_______________________________________________ >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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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(no subject)
by duhanjian＠sohu.com 11 Jun '07

11 Jun '07

  <p>Thank you for previous help.</p><p>Now I want to compare the cortical thickness of the two groups. Mr Pacheco tells me to use the group analysis to compare. When I read the manual of the group analysis (<a href="https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis">https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis</a>), I meet some problem. When writing the FSGD file, I don't how to input another group thickness (eg, control group) in to the FSGD. If not use method, how to compare the cortical thickness between the two group?</p>

2 1

volume to use for control points
by syc2114＠columbia.edu 08 Jun '07

08 Jun '07

Hi, I recently started using Freesurfer and I have a quick question about adding control points. I want to add control points to a stretch of white matter which was excluded - can I add them to the wm.mgz volume by referring to the T1 aux or do they need to be added to the brainmask volume only?

3 2

Where can I find global and local thickness / volume measures for individual subjects?
by Burmicz, Ryszarda 08 Jun '07

08 Jun '07

Hi! I am new to Freesurfer; I have run reconstruction steps with recon-all. I can find no reference to thickness values calculated as part of this process, apart from visualising them in Freesurfer - is there a specific file from which I can extract this information without running the GUI? I am comparing data from a single subject across different scanning protocols in order to look at variation in thickness. So ultimately I would like to produce tabulated data of global and local thicknesses. Many thanks for your help, Rysia

2 1

FRD in ROI
by Marie Schaer 07 Jun '07

07 Jun '07

Hello everybody, Following the question of Jorge Luis yesterday, I was wondering if the option "marked only" in "Set threshold using FDR" could be an option to get FDR corrected results on parcells of the cortical surface? However, when I load ROI and click on "marked only", the terminal window shows: "surfer: Error calculating threshold with FDR". Any hint would be very appreciated, many thanks, Marie Schaer

1 0

F-Test and directed contrasts
by Juergen Haenggi 07 Jun '07

07 Jun '07

Dear Freesurfer users We have done a cortical thickness group comparison, but we are not absolutely sure which color corresponds to which contrast. In our *.mat file we specified -1 1 0 0 0 0, but the sig.mgh file shows both directed contrasts (group1 > group2 and group1 < group2). Where can we look which color corresponds to which contrast? We searched for the answer in the archives, but did not find it! Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

2 1

w file to label
by Robert Levy 07 Jun '07

07 Jun '07

Hello, I am trying to convert a w file into a label file, and the best way I came up with seems like it is too complicated to be the actual best way. What I am doing below is reading a list of subjects, and then for each subject, 1.) running mri_surfcluster, 2.) merging its output into a new label, and 3.) removing the component labels that went into it. # entered in bash shell # generate the .w file paint-sess -sf Subject_Lists/bw-group-error-5 -analysis EMerror -contrast rACC_lh_pos_0_ASce68 -map mask -hemi lh # merge labels cat Subject_Lists/bw-group-error-5 | while read subject; do mri_surfcluster --in $subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-lh.w --thmin 0.5 --sign pos --subject $subject --hemi lh --surf orig --annot aparc --minarea 1 --sum $subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-h-label.sum --olab $subject/label/rACC_lh_pos_0_ASce68 ; cd $subject/label; mri_mergelabels $(ls rACC_lh_pos_0_ASce68*.label | sed 's/rACC/\-i rACC/g') -o rACC_lh_pos_0_ASce68.label; rm rACC_lh_pos_0_ASce68-0*.label; cd $SUBJECTS_DIR; done #check in tksurfer surf-sess -s mano001 -analysis EMerror -contrast rACC_lh_pos_0_ASce68 -map mask -hemi lh -fthresh 1 It seems to work, but if there is a more direct way, it may be better just because there is potential room for error the way I am doing it. Thanks, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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