External Email - Use Caution Thank you for your help. I cannot load the label on surface, this is the error:
[toyama-no-iMac:/applications/freesurfer/subjects] toyama% qdec Reading /applications/freesurfer/tktools/tkUtils.tcl Using /applications/freesurfer/lib/tcl/fsgdfPlot.tcl qdec.bin(41334,0xa15971a8) malloc: *** mach_vm_map(size=1149440000) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRISalloc(15124178, 76): could not allocate faces Cannot allocate memory What do you mean how many point? How do I find it? On Fri, Jan 17, 2020 at 1:17 PM Greve, Douglas N.,Ph.D. < [email protected]> wrote: > Is the label valid? Can you load it on a surface? How many points are in > it? > > On 1/16/2020 9:51 PM, Tien Pham wrote: > > External Email - Use Caution > Thank you for your e-mail. > It seems I got another error. This is what it showed in terminal: > > [toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats > --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum > sum.dat > > > > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ > > cwd > > cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh > lh.frontoinsula.label --id 1 --sum sum.dat > > sysname Darwin > > hostname toyama-no-iMac.local > > machine x86_64 > > user toyama > > UseRobust 0 > > Constructing seg from label > > Segmentation fault > > > Could you help me please? > > On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. < > [email protected]> wrote: > >> Sorry, it should have been --sum instead of --o >> the subject name is subject_id >> --id 1 just means to take the vertices in the label (--id 0 would mean to >> take the background) >> >> On 1/16/2020 7:07 PM, Tien Pham wrote: >> >> External Email - Use Caution >> Thank you very much for your e-mail. >> I tried, but this '' --o '' is unknown showing in terminal and the '' >> --id '' flag is subject name? >> Could you please help me? >> For example, I found the change in frontoinsula region between 2 groups >> in my dataset and I want to extract the values of this region. >> >> On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. < >> [email protected]> wrote: >> >>> It might be easier to use mri_segstats, eg, >>> >>> mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label >>> --id 1 --o sum.dat >>> >>> The mean value will be in the "Mean" column of the sum.dat >>> >>> >>> On 1/14/2020 7:08 PM, Tien Pham wrote: >>> >>> External Email - Use Caution >>> Dear FreeSurfer Experts, >>> >>> I am Tien Pham, I am stucked at this situation. I calculated >>> longitudinal LGI changes in my data set with two time points using >>> longitudinal pipeline. Now I would like to extract the regional LGI and >>> gray matter volume in my longitudinal results using QDEC to draw the ROIs >>> which is showed significant differences, label it and map to all subjects. >>> Then I get the LGI value of the ROI I saved before using the command below: >>> >>> cd $SUBJECTS_DIR >>> mris_anatomical_stats -l lh.untitled.label \ >>> -t lh.pial_lgi \ >>> -b \ >>> -f subject_id/stats/lh.untitled.stats subject_id lh >>> >>> And this is the result: >>> >>> [toyama-no-iMac:/applications/freesurfer/subjects] toyama% >>> mris_anatomical_stats -l lh.frontoinsula.label \ >>> >>> ? -t lh.pial_lgi \ >>> >>> ? -b \ >>> >>> ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh >>> >>> limiting computations to label lh.frontoinsula.label. >>> >>> using thickness file lh.pial_lgi. >>> >>> reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz... >>> >>> reading input surface >>> /applications/freesurfer/subjects/VC019_1/surf/lh.white... >>> >>> reading input pial surface >>> /applications/freesurfer/subjects/VC019_1/surf/lh.pial... >>> >>> reading input white surface >>> /applications/freesurfer/subjects/VC019_1/surf/lh.white... >>> >>> >>> >>> table columns are: >>> >>> number of vertices >>> >>> total surface area (mm^2) >>> >>> total gray matter volume (mm^3) >>> >>> average cortical thickness +- standard deviation (mm) >>> >>> integrated rectified mean curvature >>> >>> integrated rectified Gaussian curvature >>> >>> folding index >>> >>> intrinsic curvature index >>> >>> structure name >>> >>> >>> >>> 6595 4368 15935 3.311 0.895 0.158 0.077 135 19.7 >>> lh.frontoinsula.label >>> >>> >>> As I saw there was no columns showing the LGI value, I did similar with >>> gray matter volume, the result displayed the different in some values of >>> the columns. >>> Could you please help me to explain about this? >>> >>> Thank you very much. >>> >>> >>> Best regards, >>> >>> Tien Pham >>> >>> _______________________________________________ >>> Freesurfer mailing >>> [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing >> [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing > [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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