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30132 discussions

errors Quantifying Hippocampal Subfield Segmentations
by Carolina Valencia 30 Aug '12

30 Aug '12

Hi Freesurfer community: I run hippocampal subfields command succesfully recon-all -s CORBIC_vol15 finished without error at Thu Aug 30 11:29:16 COT 2012 done but when I run kvlQuantifyHippocampalSubfieldSegmentations.sh the terminal shows some errors: resultsDirectory /home/cvalencia/freesurfer/subjects/volumetria cd /home/cvalencia/freesurfer/subjects/volumetria resultsDirectory /home/cvalencia/freesurfer/subjects/volumetria startIndex: 1 endIndex: 5 cd CORBIC_vol15/ Quantifying subject CORBIC_vol15/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /home/cvalencia/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt cd .. Quantifying subject CORBIC_vol15/ right Doing right side cd mri kvlQuantifyPosteriorProbabilityImages /home/cvalencia/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz > volumeStats_right.txt cd .. cd .. cd fsaverage/ Quantifying subject fsaverage/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /home/cvalencia/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x9231728): Can't find/open file: posterior_Left-Hippocampus.mgz /home/cvalencia/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: línea 22: 15068 Abortado (`core' generado) kvlQuantifyPosteriorProbabilityImages /home/cvalencia/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt failed to do kvlQuantifyPosteriorProbabilityImages /home/cvalencia/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt when I tried to visualize them cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria/CORBIC_vol15$ freeview nu.mgz \ > -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ > -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ > -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt freeview.bin: No match. Am I miss something? Best regards, -- -- *Carolina Valencia M*

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Converting BV ROIs to FS
by Katie Bettencourt 30 Aug '12

30 Aug '12

So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. Katie

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Re: [Freesurfer] A question about hippocampal subfield segmentation
by Usman Khan 30 Aug '12

30 Aug '12

Hi Lijie (cc to mailing list), I wrote a script to do just this in July. Here is a link to a tar file. It requires knowledge of matlab and bash, but is pretty straight forward. It https://www.dropbox.com/s/s1f78j2ozv1gw8q/subfield_to_ROI.tar.gz a) transforms the subfield probabilities to nu.mgz space (bash, using mri_label2vol) b) applies a threshold to the maps (Koen suggested 50% of max probability, hence 128 of 255) to avoid over-estimation of the subfield volumes (bash) c) comparing the probabilities of individual subfields in IJK space and assigning a unique label to each subfield We can continue this discussion off-line if you like

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Mask in Qdec analyses
by Tate, David Franklin 30 Aug '12

30 Aug '12

I want to be able to use a mask in some of the cortical thickness studies so as to reduce the number of comparisons being conducted as well as to be more hypothesis driven. Can anyone provide some guidance on whether or not this can be accomplished? Thanks, David

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crash repport automatic hippocampus segmentation failed
by Knut J Bjuland 30 Aug '12

30 Aug '12

When I run subfield segmentation for some of the subject, I get segmentation error. Is there any known workaround these problems as recon-all is ran on a cluster? I usually get this error Rasterizing Levenberg-Marquardt.../global/apps/freesurfer/5.1.0/bin/kvlSegmentHippocampalSubfields.sh: line 18: 9231 Segmentation fault kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txtfailed to do kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txtCan I edit kvlSegmentHippocampalSubfields.sh to ensure that it does not exit the loop at line 18.Knut J

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hippocampal subfield segmentation
by Carolina Valencia 30 Aug '12

30 Aug '12

Hi Freesurfer community, A quick question, how long takes to run the hippocampal subfield segmentation for a subject that has already run the typical recon-all pipeline? Thank you, -- -- *Carolina Valencia M *

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A question about hippocampal subfield segmentation
by soft.join Huang 30 Aug '12

30 Aug '12

Hi, freesurfer experts, I have a question about how to convert a segmented hippocampal subfield file into a ROI. After -hippo-subfields processing using recon-all command, I have got several files named posterior_left/right_**.mgz. And the segmented volume just coverd a small area in subject's whole brain volume. Now i want to convert the segented volume into subject's whole brain volume space and I can use it as a ROI. Is there any solution to do that? Hope for the reply. Best regards, Lijie Huang

1 0

(no subject)
by Marie Schneider 30 Aug '12

30 Aug '12

Dear FreeSurfer expects, I ran a cortical thickness analysis that revealed many significant clusters, but half of them are pretty small. Is there a possibility in qdec to display only clusters with a certain clustersize on the inflated surface? Thank you very much for your help, best wishes, Marie

1 0

freeview tracula error
by Cat Chong 29 Aug '12

29 Aug '12

Dear Experts: I have worked my way through Tracula and things seem to work fine, but when I try to view my tractography outputs I get the following persistent error using freeview (copied below). I am using a Mac OS X 10.6.7. freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Could this be a similar problem as described below? http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22110.html And if so, would this be a similar fix? Cheers, cat Below is the error message I get: freeview -v $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dmri/dtifit_FA.nii.gz \ > $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dpath/5cpts/priormni/seg14/initmni/regflt/lh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' \ > $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dpath/5cpts/priormni/seg14/initmni/regflt/rh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' & [1] 24711 fmris-Mac-Pro-2:8000_tracula fmri$ 2012-08-29 12:51:30.566 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.571 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.593 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.596 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.616 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.619 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.640 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.643 freeview.bin[24711:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool))

2 2

mri_watershed and other errors.
by Darren R Gitelman 29 Aug '12

29 Aug '12

Hi I am having a problem getting recon-all to finish on 1 subject. The first time I ran recon-all -all I got an mri_watershed error. (see attached log). Based on one of the posts to the list I then ran: recon-all -skullstrip -no-wsgcaatlas -s <subj id> This completed successfully. Then I ran: recon-all -autorecon2 -autorecon3 -s <subj id> This did not complete successfully with the error that it can't find the brain.mgz file. I did look at the orig.mgz and T1.mgz files and they look fine. The talairach transform I think is also fine. What do I do about this? Thanks, Darren

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