Freesurfer

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Freesurfer-Error message
by Varghese Chikku 03 Sep '12

03 Sep '12

Hi, While running the following command: recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre -subjid test2 I keep seeing the following error: ... corRead(): can't open file /media/sf_freesurferstudys/raw/raw_scr/T1pre/COR-.info $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /media/sf_freesurferstudys/raw/raw_scr/T1pre... Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 EDT 2012 My image files, in dcm format, are at /media/sf_freesurferstudys/raw/raw_scr/T1pre : /media/sf_freesurferstudys/raw/raw_scr/T1pre> ls Image00001 Image00010 Image00019 Image00028 Image00037 Image00046 Image00002 Image00011 Image00020 Image00029 Image00038 Image00047 Image00003 Image00012 Image00021 Image00030 Image00039 Image00048 Image00004 Image00013 Image00022 Image00031 Image00040 Image00049 Image00005 Image00014 Image00023 Image00032 Image00041 Image00050 Image00006 Image00015 Image00024 Image00033 Image00042 Image00007 Image00016 Image00025 Image00034 Image00043 Image00008 Image00017 Image00026 Image00035 Image00044 Image00009 Image00018 Image00027 Image00036 Image00045 Many thanks for your help. chikku

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Fwd: Command line to get BA stats with the thresholds
by _andreia_＠sapo.pt 31 Aug '12

31 Aug '12

Hi! I'm reposting my question: Is there a command line to obtain the BA values with the recommended thresholds (e.g. 0.9 for V1) from all subjects at once? At least for each area at once for all subjects? Thank you, Andreia Pereira

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(no subject)
by Ryan 31 Aug '12

31 Aug '12

Hello all, I'm analyzing the data for a training study our research group conducted, and I'm looking to see if there are changes in cortical thickness as a result of training. We have pre- and post-training scans, so I followed the longitudinal tutorial ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#In…) There are 4 measures listed on the website (average, rate, pc1, and spc) - which do I choose if I simply want to see if there is a difference in cortical thickness for pre vs. post? Also, do I need to run anything afterwards such as cluster corrections? Best, -W. Ryan McGarry

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Loading nifti overlays with TCL script
by Sid Kundu 31 Aug '12

31 Aug '12

Hello Freesurfers, I have a basic question as I'm just getting into scripting, but I'm trying to write a script that loads overlays from multiple contrasts and takes images. However, I can't figure out how to properly load nifti files as overlays. I'm attempting to load .nii volumes from group level analysis (which should need no registration file), so when I use sclv_read_from_volume setting the argument for registration type to 1 or 2 (look for register.dat, or calculate identity) both fail. Any help on this would be much appreciated. Thanks in advance. _________________________________ Sid Kundu Biomedical Engineering Boston University

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scale bar shrink/grow problem if fsaverage is displayed
by Jörg Pfannmöller 31 Aug '12

31 Aug '12

Dear freesurfers, if I display fsaverage in tksurfer (tksurfer fsaverage rh pial) and switch on the scale bar it appears to have a length of approximately 1 cm. However, If I start to zoom into the brain the color bar shrinks until a certain scale-up is reached. After it has completely vanished it starts to grow if I further scale-up the image. If I use a subject from our investigations this problem does not ocur. Can someone give my a hint about the cause of this problem? Cheers pfannmoe

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I: hippocampal subfield segmentation
by lorenzo pasquini 30 Aug '12

30 Aug '12

hello carolina to me it took about 5-6 hours. greets, lorenzo ________________________________ Da: Carolina Valencia <cvalencia(a)linkdx.com.co> A: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> Inviato: Giovedì 30 Agosto 2012 20:37 Oggetto: [Freesurfer] hippocampal subfield segmentation 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 _______________________________________________ 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.

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how to convert .vtk surface meshes with labels to .annot format?
by Arno Klein 30 Aug '12

30 Aug '12

what is the best way to convert a .vtk surface mesh (with labels as scalars) to freesurfer .annot format? i am currently converting the vtk file to freesurfer .label files, then using freesurfer to consolidate these into an .annot file, which is slow, roundabout, and generates a lot of files. cheers, @rno

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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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