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
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 list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. < 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:
External Email - Use CautionDear 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 name6595 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 listFreesurfer@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
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. <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:
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 list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. < 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:
External Email - Use CautionThank 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.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 CautionDear 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 name6595 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 listFreesurfer@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 listFreesurfer@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
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. <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:
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. <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:
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 list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. < 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:
External Email - Use CautionThank 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.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 CautionThank 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.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 CautionDear 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 name6595 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 listFreesurfer@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 listFreesurfer@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 listFreesurfer@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
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. <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:
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. <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:
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. <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:
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 list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. < 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:
External Email - Use CautionThank 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.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 CautionThank 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.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 CautionThank 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.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 CautionDear 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 name6595 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 listFreesurfer@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 listFreesurfer@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 listFreesurfer@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 listFreesurfer@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
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:
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. <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:
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. <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:
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. <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:
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. <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:
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 list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
Thank you for your e-mail. Yes, of course. I send the label I created to you in attachment. Please, let me know if you have any problem with it. Thank you.
On Sat, Jan 25, 2020 at 12:24 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
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:
External Email - Use CautionThank 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.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 CautionThank 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.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 CautionThank 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.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 CautionThank 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.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 CautionDear 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 name6595 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 listFreesurfer@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 listFreesurfer@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 listFreesurfer@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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I cannot see anything wrong with the label. How did you create it? Are you sure that the label belongs to the same subject's surface that you loading it onto?
On 1/26/2020 12:10 AM, Tien Pham wrote:
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Thank you for your e-mail. Yes, of course. I send the label I created to you in attachment. Please, let me know if you have any problem with it. Thank you.
On Sat, Jan 25, 2020 at 12:24 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: 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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Thank you for your response. I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much.
Sorry, I do not have the previous emails, can you repost with previous emails in the message?
On 1/28/2020 7:35 PM, Tien Pham wrote:
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Thank you for your response. I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much.
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Thank you for your response. I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much.
On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Sorry, I do not have the previous emails, can you repost with previous emails in the message?
On 1/28/2020 7:35 PM, Tien Pham wrote:
External Email - Use CautionThank you for your response.
I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much.
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Can you read my message? I used longitudinal pipeline for my data set with two time points and measured the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on the subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you very much.
On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Sorry, I do not have the previous emails, can you repost with previous emails in the message?
On 1/28/2020 7:35 PM, Tien Pham wrote:
External Email - Use CautionThank you for your response.
I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much.
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sorry for the delay. You will have to use mri_label2label to map the label from the fsaverage space to the individual space
On 1/31/2020 10:01 PM, Tien Pham wrote:
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Can you read my message? I used longitudinal pipeline for my data set with two time points and measured the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on the subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you very much.
On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Sorry, I do not have the previous emails, can you repost with previous emails in the message? On 1/28/2020 7:35 PM, Tien Pham wrote:External Email - Use Caution Thank you for your response. I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you for your email. I run exactly the command mri_label2label as you suggested, and the command finished without any problem. But I did not know why I could not open the label. Please help me. Thank you once again.
On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
sorry for the delay. You will have to use mri_label2label to map the label from the fsaverage space to the individual space
On 1/31/2020 10:01 PM, Tien Pham wrote:
External Email - Use CautionCan you read my message? I used longitudinal pipeline for my data set with two time points and measured the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on the subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you very much.
On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Sorry, I do not have the previous emails, can you repost with previous emails in the message?
On 1/28/2020 7:35 PM, Tien Pham wrote:
External Email - Use CautionThank you for your response.
I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much.
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What tool are you trying to use to load the label? What happens when you try?
On 2/7/2020 10:11 PM, Tien Pham wrote:
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Thank you for your email. I run exactly the command mri_label2label as you suggested, and the command finished without any problem. But I did not know why I could not open the label. Please help me. Thank you once again.
On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
sorry for the delay. You will have to use mri_label2label to map the label from the fsaverage space to the individual space On 1/31/2020 10:01 PM, Tien Pham wrote:External Email - Use Caution Can you read my message? I used longitudinal pipeline for my data set with two time points and measured the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on the subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you very much. On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Sorry, I do not have the previous emails, can you repost with previous emails in the message? On 1/28/2020 7:35 PM, Tien Pham wrote:External Email - Use Caution Thank you for your response. I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you for your email. I tried to load the label with qdec and freeview and both were not worked. When i tried with qdec, It said '' load the surface first '' then I did but It did not work and showed some errors. The other way when I tried to load with qdec, qdec was closed suddenly without any notification. I am looking forward to hearing from you.
On Fri, Feb 14, 2020 at 11:44 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
What tool are you trying to use to load the label? What happens when you try?
On 2/7/2020 10:11 PM, Tien Pham wrote:
External Email - Use CautionThank you for your email. I run exactly the command mri_label2label as you suggested, and the command finished without any problem. But I did not know why I could not open the label. Please help me. Thank you once again.
On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
sorry for the delay. You will have to use mri_label2label to map the label from the fsaverage space to the individual space
On 1/31/2020 10:01 PM, Tien Pham wrote:
External Email - Use CautionCan you read my message? I used longitudinal pipeline for my data set with two time points and measured the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on the subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you very much.
On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Sorry, I do not have the previous emails, can you repost with previous emails in the message?
On 1/28/2020 7:35 PM, Tien Pham wrote:
External Email - Use CautionThank you for your response.
I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much.
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Try using freeview
On 2/18/2020 8:17 PM, Tien Pham wrote:
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Thank you for your email. I tried to load the label with qdec and freeview and both were not worked. When i tried with qdec, It said '' load the surface first '' then I did but It did not work and showed some errors. The other way when I tried to load with qdec, qdec was closed suddenly without any notification. I am looking forward to hearing from you.
On Fri, Feb 14, 2020 at 11:44 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
What tool are you trying to use to load the label? What happens when you try? On 2/7/2020 10:11 PM, Tien Pham wrote:External Email - Use Caution Thank you for your email. I run exactly the command mri_label2label as you suggested, and the command finished without any problem. But I did not know why I could not open the label. Please help me. Thank you once again. On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: sorry for the delay. You will have to use mri_label2label to map the label from the fsaverage space to the individual space On 1/31/2020 10:01 PM, Tien Pham wrote:External Email - Use Caution Can you read my message? I used longitudinal pipeline for my data set with two time points and measured the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on the subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you very much. On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Sorry, I do not have the previous emails, can you repost with previous emails in the message? On 1/28/2020 7:35 PM, Tien Pham wrote:External Email - Use Caution Thank you for your response. I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you for your suggestion. I tried to use freeview to load surface on the label I created. But terminal showed this error '' freadFloat: fread failed '' many times. I tried to load label with qdec and I got the error (pic 1) I attached below. I also tried to load surface with qdec and this error displayed in terminal (pic 2). I am very appreciated when you helped me before. I am looking forward to hearing from you. Thank you very much.
On Mon, Feb 24, 2020 at 11:16 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Try using freeview
On 2/18/2020 8:17 PM, Tien Pham wrote:
External Email - Use CautionThank you for your email. I tried to load the label with qdec and freeview and both were not worked. When i tried with qdec, It said '' load the surface first '' then I did but It did not work and showed some errors. The other way when I tried to load with qdec, qdec was closed suddenly without any notification. I am looking forward to hearing from you.
On Fri, Feb 14, 2020 at 11:44 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
What tool are you trying to use to load the label? What happens when you try?
On 2/7/2020 10:11 PM, Tien Pham wrote:
External Email - Use CautionThank you for your email. I run exactly the command mri_label2label as you suggested, and the command finished without any problem. But I did not know why I could not open the label. Please help me. Thank you once again.
On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
sorry for the delay. You will have to use mri_label2label to map the label from the fsaverage space to the individual space
On 1/31/2020 10:01 PM, Tien Pham wrote:
External Email - Use CautionCan you read my message? I used longitudinal pipeline for my data set with two time points and measured the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on the subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you very much.
On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Sorry, I do not have the previous emails, can you repost with previous emails in the message?
On 1/28/2020 7:35 PM, Tien Pham wrote:
External Email - Use CautionThank you for your response.
I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much.
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what is your command line?
On 3/5/2020 1:50 AM, Tien Pham wrote:
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Thank you for your suggestion. I tried to use freeview to load surface on the label I created. But terminal showed this error '' freadFloat: fread failed '' many times. I tried to load label with qdec and I got the error (pic 1) I attached below. I also tried to load surface with qdec and this error displayed in terminal (pic 2). I am very appreciated when you helped me before. I am looking forward to hearing from you. Thank you very much.
On Mon, Feb 24, 2020 at 11:16 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Try using freeview On 2/18/2020 8:17 PM, Tien Pham wrote:External Email - Use Caution Thank you for your email. I tried to load the label with qdec and freeview and both were not worked. When i tried with qdec, It said '' load the surface first '' then I did but It did not work and showed some errors. The other way when I tried to load with qdec, qdec was closed suddenly without any notification. I am looking forward to hearing from you. On Fri, Feb 14, 2020 at 11:44 PM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: What tool are you trying to use to load the label? What happens when you try? On 2/7/2020 10:11 PM, Tien Pham wrote:External Email - Use Caution Thank you for your email. I run exactly the command mri_label2label as you suggested, and the command finished without any problem. But I did not know why I could not open the label. Please help me. Thank you once again. On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: sorry for the delay. You will have to use mri_label2label to map the label from the fsaverage space to the individual space On 1/31/2020 10:01 PM, Tien Pham wrote:External Email - Use Caution Can you read my message? I used longitudinal pipeline for my data set with two time points and measured the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on the subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you very much. On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Sorry, I do not have the previous emails, can you repost with previous emails in the message? On 1/28/2020 7:35 PM, Tien Pham wrote:External Email - Use Caution Thank you for your response. I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on subjects in cross, base, long steps but it did not work. I am looking forward to hearing from you. Thank you so much. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Greve, Douglas N.,Ph.D.
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Tien Pham