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Qdec error
by Kairys, Anson 29 Jun '12

29 Jun '12

I got an error beginning with this. Thanks for any help Error in analyze: command failed: mri_glmfit --y /<mypath>/qdec/LH_insula_thick/y.mgh --fsgd ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Re: [Freesurfer] trac-all: error during trac-paths due to tract missing
by Anastasia Yendiki 29 Jun '12

29 Jun '12

Hi Torben - I'm looking at all the invocations of "trac-all -prep" in your log file, and they've both exited with an error (the same bvecs error). > grep prep trac-all.log -prep -c /Users/torben/Desktop/tracon/tracon New invocation of trac-preproc /Applications/MRSoftware/freesurfer/bin/trac-preproc trac-preproc exited with ERRORS at Do 21 Jun 2012 20:34:41 CEST ... -prep -c /Users/torben/Desktop/tracon/tracon New invocation of trac-preproc /Applications/MRSoftware/freesurfer/bin/trac-preproc trac-preproc exited with ERRORS at So 24 Jun 2012 22:37:30 CEST After that you've ran "trac-all -bedp" and "trac-all -path", but obviously these are going to fail if "trac-all -prep" has failed. I hope this makes sense. a.y On Fri, 29 Jun 2012, Torben Prokscha wrote: > Hi Anastasia! > > Yes, we reran trac-all -prep after fixing the bvec issue. I am still > surprised how you know that the latest failure was due to a bvecs problem, > because the last error message was the one about the missing tract ...? > > Thank you for your help! > > Best > Torben > > >> >> Hi Torben - I just scrolled to the end of your log file. The last >> invocation of trac-all -prep is the one that failed b/c of the bvecs >> error. Did you rerun trac-all -prep after you fixed the bvecs? >> >> Thanks, >> a.y >> >> On Tue, 26 Jun 2012, Torben Prokscha wrote: >> >>> Hi Priti, >>> >>> thank you for your reply, but I'm afraid you didn't scroll to the end of >>> the log file: Yes, we had that bvecs/bvals error in the first run, but >>> we >>> corrected it and got the error I reported in my previous mail (it is >>> also >>> printed at the end of the log file): >>> >>> ERROR: Could not open >>> /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt >>> >>> Could you or anybody else please help with this problem which is >>> obviously >>> related to missing tracts? >>> >>> Thanks in advance >>> Torben >>> >>> >>>> Hi Torben, >>>> >>>> Your trac-preproc exited with errors because of the following error. >>>> >>>> Error: bvecs and bvals don't have the same number of entries >>>> >>>> You should check to see if your bvals and bvecs have the same no.of >>>> lines >>>> and then rerun trac-all -prep. >>>> >>>> Priti >>>> >>>> >>>>> Dear all, >>>>> >>>>> while running trac-all, I got the following error: >>>>> >>>>> ERROR: Could not open >>>>> /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt >>>>> >>>>> Obviously, a similar problem was discussed before (here: >>>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019570.h…) >>>>> However, no general solution was publicly mailed. Since it was >>>>> requested >>>>> then, I attach the trac-all.log file. >>>>> >>>>> Thanks in advance for any help! >>>>> >>>>> Best >>>>> Torben Prokscha >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >> > > > >

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error longitudinal processing
by j janssen 29 Jun '12

29 Jun '12

Hi (Martin), - version 5.1 (Ubuntu 64b) - command: long_mris_slopes --qdec ./qdec/long.qdec.table.n114.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time ISI_years --qcache fsaverage - attached: first 3 lines of qdec table containing the info for subject 11298 - attached: on screen error output. - i have 2 timepoints/subject. things go awry in the "SUBJECT 11298 Running Within-Subject GLM" step (see attachment): Reshaping mriglm->mask... ERROR: mri_reshape: number of elements cannot change what am i doing wrong? -joost

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Glmfit subtraction between 2 individuals
by Adam Nitenson 29 Jun '12

29 Jun '12

Hi all, I am trying to visualize the surface map showing the Post Treatment - Pre Treatment cortical thickness in a single subject. The Post and Pre scans are processed like 2 separate subjects. I used the commands: mris_preproc --f /cluster/roffman/users/Stable5_PerRun/Subject_Files/FB12_Pairs/FB0011040 --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/FB12_Pairs/FB0011040/THICKNESS-MAP-LH.mgh and mri_glmfit --y /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/FB12_Pairs/FB0011040/THICKNESS-MAP-LH.mgh --fsgd /cluster/roffman/users/fsgd/FB12_Pairs/FB0011040.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/FB12_Pairs/FB0011040/Post_Minus_Pre/LH --surf fsaverage lh --fwhm 4.6 The subject and fsgd lists only have 2 subjects (the post and the pre) and the contrast is the 1 -1, same as the group.diff.mtx on the Wiki. I receive the error DOF = 0, which is likely because each group only has 1 subject. Usually I have multiple subjects in each group. Is there an alterate way to generate this difference map when only using 2 subjects?? Best, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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lh.pial question
by Borzello, Mia 29 Jun '12

29 Jun '12

Hi all, Is there a way to edit the pial files (e.g. lh.pial)? I want to delete a few vertices we think are causing errors for a 3D printing we are trying to do. Thanks, m

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surface vertex pairs; voxel coloring for tkmedit
by John Papaioannou 29 Jun '12

29 Jun '12

Hi, In regard to the surface files, is it correct to say that the wm and pial vertices correspond to each other (e.g., wm vertex # 12345 corresponds to pial vertex # 12345 as the minimum distance between the two surfaces), and so have the same number of vertices? Also, I would like to "colorize" voxels, but not for segmentation. Instead, colored voxels would represent various metric "anomalies". It's rather easy with curv files for 3D display (positive or negative values at vertex), but I want to show this on tkmedit in 2D. Could you explain what is the easiest way to do this? Thanks, John ___ John Papaioannou Medical Imaging Sciences Digital Mammography, CAD Mammography Department of Radiology Biological Sciences Division The University of Chicago 5841 South Maryland Avenue Chicago, Illinois 60637 773.834.5104 voice 773.702.0371 fax

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Freeview scripting reference
by Inge Kasbohm Amlien 29 Jun '12

29 Jun '12

Hi list, I am looking for a complete reference to scriptable commands for Freeview, comparable to what exists for tksurfer (e.g. http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferScripting/Tk…) Does this exist? Thanks! ___________________________________ Inge Kasbohm Amlien E-mail: inge.amlien(a)psykologi.uio.no Phone: +47 97106525 Psychologist // Ph.D candidate Centre for the Study of Human Cognition Department of Psychology, University of Oslo

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ROI from left to right hemi - cortical thickness
by Irene Altarelli 29 Jun '12

29 Jun '12

Dear all, I have a ROI on the left hemisphere and I'd like to extract cortical thickness values from the homologous region in the right hemisphere. For this I applied the interhemispheric registration process and got my ROI mapped into the right hemisphere in /subject/xhemi/label. However when I tried to run mris_anatomical_stats on /subject/xhemi it failed, as there is no wm.mgz file in /subject/xhemi/mri. Any suggestion would be greatly appreciated. Thank you, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23

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mri_robust_template- Segmentation Fault
by Usman Khan 28 Jun '12

28 Jun '12

Hi there Freesurfer, I am running into a seg fault while running mri_robust_template on freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on a Centos6.2 build. Thinking that this may perhaps be an OS-related issue, I tried to download FS binaries from http://www.freesurfer.net/pub/dist/freesurfer/misc/linux-centos6_x86_64/ but the link is dead Any help would be appreciated Usman $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --satit: Will estimate SAT iteratively! --mov: Using 191_0001.nii.gz as movable/source volume. --mov: Using 192_0001.nii.gz as movable/source volume. Total: 2 input volumes --template: Using test.nii.gz as template output volume. reading source '191_0001.nii.gz'... reading source '192_0001.nii.gz'... Segmentation fault (core dumped)

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Pial and WM boundary edits
by Skyler Gabriel Shollenbarger 28 Jun '12

28 Jun '12

To whom it may concern, After running autorecon2 (recon-all -subjid xxxxxxxx -autorecon2) there were areas that required correcting for both the pial and WM boundaries. I added control points to correct the WM boundaries and saved them using File > Save Control Points. I also used the select voxels tool to extend the boundaries in areas where the pial surface was not generous enough resulting in excluded GM and saved them using File > Save Volume. After adding these voxels and control points I ran (recon-all -autorecon-pial -subjid xxxxxxxx) however received an error that '-autorecon-pial' was not recognized. Then, in attempt to regenerate the boundaries with the new voxels and control points saved, I ran (recon-all -subjid xxxxxxxx -autorecon2-cp). When reloading the image to inspect the new boundaries using command (tkmedit xxxxxxxx brainmask.mgz -surfs -segmentation wm.mgz $FREESURFER_HOME/ASegStatsLUT.txt), I found that the errors were not fixed. If anyone has insight into what I'm doing incorrectly it would be much appreciated! Skyler -- Skyler G. Shollenbarger Graduate Student Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee

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