External Email - Use Caution Thank you for your e-mail. I also could not load the label in freeview. The terminal showed the following error:
2020-01-22 09:56:18.064 Freeview[51338:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: 2020-01-22 09:56:26.655 Freeview[51338:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: freadFloat: fread failed freadFloat: fread failed This error was still showing like it never end until I close freeview. I draw the ROI in qdec, then add selection to ROI , and save the current label. That was how I created the label. I am looking forward to hearing from you. Thank you. On Wed, Jan 22, 2020 at 12:17 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > You can try freeview, but there might be something wrong with the label. > How was it created? > > On 1/16/2020 11:51 PM, Tien Pham wrote: > > 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. < > dgr...@mgh.harvard.edu> 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. < >> dgr...@mgh.harvard.edu> 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. < >>> dgr...@mgh.harvard.edu> 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 >>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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