Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

missing ROI when using mri_label2vol to transfer ic2.tri
by Leon 05 Sep '12

05 Sep '12

Hi, folks when I transferred the annotation file obtained using mri_make_face_parcellation based on ic2 (162 labels) to a volume file using mri_label2vol, I found that one ROI patch was missing in the volume file (see attached). I searched archives and the closest thread I could found is that somebody reported an ROI with the last index was missing in the mgz file after they were transferred from the annotation file to the volume file. Could someone help on this? If this happens to be a bug, is there any other strategy that will allow me to get a GM/WM ribbon without a hole on it? Many thanks in advance Leon

5 17

nu_correct problem
by rega0026＠umn.edu 10 Jul '12

10 Jul '12

Hello, I am trying to run recon-all using freesurfer 5.1.0. This worked on most of my subjects, but for about 10 subjects, I got an error: nu_correct: Command not found I can see on the archive that several others have run into this problem, but I couldn't figure out from the archives what the solution is. I do have perl installed in usr/bin. Thanks very much, Katie -- Kathryn R. Cullen, M.D. Assistant Professor University of Minnesota Medical School Department of Psychiatry Division of Child and Adolescent Psychiatry (612) 273-9825

4 4

label transformation to MNI space
by Linda Douw 05 Jul '12

05 Jul '12

Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Linda Douw, PhD.

4 7

Extraction Longitudinal Stats
by Dídac Vidal 04 Jul '12

04 Jul '12

Hi everybody, I have a question about FS longitudinal post-processing. Currently I obtained some corrected results comparing a Control vs. an Experimental group (pre-post). What i would like to know is if there's a thinning in the control group or a increase in the thickness of the experimental group. I tought in create a label and extract the individual values of both timepoints and then do a t test in order to see if the mean differs to 0. How I can do that?; There is an easier way to do it? Thanks in advance -- Dídac Vidal Piñeiro Dept. Psychiatry and Clinical Psychobiology Faculty of Medicine University of barcelona

4 8

Hippocampal segmentation doubts
by Gabriel Gonzalez Escamilla 04 Jul '12

04 Jul '12

2 1

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

2 1

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

1 0

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 >>> >>> >>> >> > > > >

1 0

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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Freesurfer June 2012