I'm guessing that there is something wrong with the label. Can you send it?
On 1/21/2020 8:08 PM, Tien Pham wrote:
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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. <DGREVE@mgh.harvard.edumailto:DGREVE@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:
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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. <DGREVE@mgh.harvard.edumailto:DGREVE@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:
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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. <DGREVE@mgh.harvard.edumailto:DGREVE@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:
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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. <DGREVE@mgh.harvard.edumailto:DGREVE@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:
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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
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