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30132 discussions

Talairach transform/coordinates not present in mgz files and/or not shown in tkmedit
by Andrew R. Dykstra 01 Jul '12

01 Jul '12

Dear Freesurfers, I am experiencing a strange issue when processing some, but not all, subjects with the recommended recon stream. After autorecon1, which includes Talairach registration step, I cannot see Talairach coordinates in the tkmedit interface ('none' appears in the text box where the coordinates usually are - attached screenshot). This is despite the registration step supposedly succeeding (I can view and adjust the reg with tkregister2). I think this may be causing further problems when trying to compute the forward solution in MNE (I get messages there about not being able to read the coordinate transformation). Has anyone experienced an issue like this? Cheers, Andy -- Andrew R. Dykstra, PhD Auditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov

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can I run recon-all in parallel
by Dian "Oscar" Jiao 30 Jun '12

30 Jun '12

Hi, I am new to freesurfer. It seems recon-all is the most time-consuming command. I tried to run it on a HPC cluster with MPI and got the error "ERROR: it appears that recon-all is already running and re-run" and the job stopped right away. Is the code even parallelized? I had no problem running the same job on a single processor. ~Oscar

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Qdec Error (more/better info)
by Kairys, Anson 29 Jun '12

29 Jun '12

Hi everyone, I got the error I just mentioned. Terminal window says "no contrasts specified". I am trying to use "timepoint" (1-4) as a discrete factor to look at thickness across time. I guess I will have to resort to longitudinal processing? Thanks for the help -Anson ********************************************************** 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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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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