Freesurfer August 2012

freesurfer@nmr.mgh.harvard.edu

110 participants
170 discussions

error in long_mris_slopes command
by Shannon Kogachi 04 Sep '12

04 Sep '12

Hi Freesurfers, I've just tried to use the long_mris_slopes command on some longitudinal data. I've created my long.qdec.table.dat file. I've run this command before without any problems but I need to re-run it again. This time when I try to re-run it this error pops up: ERROR 1 : mris_label_calc intersect did not work? Is there any way to fix this? it also tells me the following: cp: target 'path/subjectID/lh.long.cortex.label' is not a directory Please let me know if there is any way to fix this. thank you!! -Shannon K.

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how i can compute volume of a VOI
by Eustratios Karavasilis 03 Sep '12

03 Sep '12

Dear all, i am new Freesurfer user (Freesurfer 5.0 installed). I want to calculate the volume of a VOI that is not calculated from recon all. I ll decribe you the steps that were followed. Using tkmedit and tkmedit tools i created ROIs in many slices. Every ROI i saved it as label, then i merge all the labels using the mri_mergelabels. I am trying create a volume from this "final" label using mri_label2vol, using as label the new "final" label, as template volume the origin volume (orig.mgz) but i don't have the register.dat file. How i can create it? The above way is the appropriate way to calculate a VOI? Thank you in advance!

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cortical volume and ortical jacobian_whitematter
by Knut J Bjuland 03 Sep '12

03 Sep '12

Hi,I have looked into cortical surface volume and cortical jacobian_whitematter. Can I use these measure a in similar way as cortical thickness? Do jacobian_whitematter represent the whitematter thickness in the cortex? How reliable are cortical volumes compared to cortical thickness?Best regardKnut J

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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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Freesurfer August 2012