muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh limiting computations to label /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. computing statistics for each annotation in aparc.a2009s.annot. outputting results to outSUB1_lhVOL2... reading volume /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... reading input surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading input pial surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... reading input white surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Segmentation fault: 11
On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni asabbineni@mrn.org wrote:
Good morning!
I was trying to run the mris_anatomical_stats command and for some subjects I keep getting Segmentation fault:11 error.
Some of the posts in the archive suggested that I run the recon-all command since it usually means that subjects surfaces are out of sync SO I RERAN RECON_ALL(which created the stats). Then I reran the mris_anatomical_stats command and got the segmentation fault again.
The command im using is
mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh
A little background on the new.label. We got the label by doing a regression in qdec at FDR 0.05 which created cluster and peak cluster label.
Can anyone please provide me some insight on how to trouble shoot this problem?
Thank you!
Rupa
Can you verify that the label does actually have label points in it? Just open it in a text editor or cat it to a terminal. If it does have points, send it to me. Also let me know which version of FS you are running.
doug
On 3/17/14 5:35 PM, Rupa Sabbineni wrote:
muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh limiting computations to label /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. computing statistics for each annotation in aparc.a2009s.annot. outputting results to outSUB1_lhVOL2... reading volume /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... reading input surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading input pial surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... reading input white surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Segmentation fault: 11
On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni <asabbineni@mrn.org mailto:asabbineni@mrn.org> wrote:
Good morning! I was trying to run the mris_anatomical_stats command and for some subjects I keep getting Segmentation fault:11 error. Some of the posts in the archive suggested that I run the recon-all command since it usually means that subjects surfaces are out of sync SO I RERAN RECON_ALL(which created the stats). Then I reran the mris_anatomical_stats command and got the segmentation fault again. The command im using is mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh A little background on the new.label. We got the label by doing a regression in qdec at FDR 0.05 which created cluster and peak cluster label. Can anyone please provide me some insight on how to trouble shoot this problem? Thank you! Rupa-- Rupa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug
Attached is a label file.
The FS version is freesurfer-Darwin-lion-stable-pub-v5.3.0
Here's some background information, that might be helpful.
We had 5 label files (2 for rh and 3 for lh) and 600 subjects.
I batched 600 subjects to run for each label file with the mris_anatomical_stats command.
It successfully ran for ~500 subjects. ~60 subjects didnt run at all across all 5 labels. and then there are ~40 subjects that ran for some labels and didnt run for some and I dont really see a pattern. All 100 subjects that didnt run(60 that didnt run at all and 40 that ran for some labels) all had the segmentation error.
Thank you for you help!
rupa
***************
Can you verify that the label does actually have label points in it? Just open it in a text editor or cat it to a terminal. If it does have points, send it to me. Also let me know which version of FS you are running.
doug
On 3/17/14 5:35 PM, Rupa Sabbineni wrote:
- muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l
*>* new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh *>* limiting computations to label *>* /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. *>* computing statistics for each annotation in aparc.a2009s.annot. *>* outputting results to outSUB1_lhVOL2... *>* reading volume *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... *>* reading input surface *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... *>* reading input pial surface *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... *>* reading input white surface *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... *>* reading colortable from annotation file... *>* colortable with 76 entries read (originally *>* /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) *>* Segmentation fault: 11 *>>>* On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni <asabbineni at mrn.org https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer *>* <mailto:asabbineni at mrn.org https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> wrote: *>>* Good morning! *>>>* I was trying to run the mris_anatomical_stats command and for some *>* subjects I keep getting Segmentation fault:11 error. *>>* Some of the posts in the archive suggested that I run the *>* recon-all command since it usually means that subjects surfaces *>* are out of sync SO I RERAN RECON_ALL(which created the stats). *>* Then I reran the mris_anatomical_stats command and got the *>* segmentation fault again. *>>>* The command im using is *>>* mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log *>* outSUB1_lhVOL2 SUB1 lh *>>>* A little background on the new.label. We got the label by doing a *>* regression in qdec at FDR 0.05 which created cluster and peak *>* cluster label. *>>>* Can anyone please provide me some insight on how to trouble shoot *>* this problem? *>>* Thank you! *>>* Rupa *>>>>>* -- *>* Rupa *>
On Mon, Mar 17, 2014 at 3:35 PM, Rupa Sabbineni asabbineni@mrn.org wrote:
muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh limiting computations to label /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. computing statistics for each annotation in aparc.a2009s.annot. outputting results to outSUB1_lhVOL2... reading volume /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... reading input surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading input pial surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... reading input white surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Segmentation fault: 11
On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni asabbineni@mrn.orgwrote:
Good morning!
I was trying to run the mris_anatomical_stats command and for some subjects I keep getting Segmentation fault:11 error.
Some of the posts in the archive suggested that I run the recon-all command since it usually means that subjects surfaces are out of sync SO I RERAN RECON_ALL(which created the stats). Then I reran the mris_anatomical_stats command and got the segmentation fault again.
The command im using is
mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh
A little background on the new.label. We got the label by doing a regression in qdec at FDR 0.05 which created cluster and peak cluster label.
Can anyone please provide me some insight on how to trouble shoot this problem?
Thank you!
Rupa
-- Rupa
It looks like this label was created on fsaverage. Is that the case? If so, then you need to run mri_label2label to map it into the space of an individual, then run mris_anatomical_stats doug
On 03/18/2014 12:59 PM, Rupa Sabbineni wrote:
Hi Doug Attached is a label file. The FS version is freesurfer-Darwin-lion-stable-pub-v5.3.0 Here's some background information, that might be helpful. We had 5 label files (2 for rh and 3 for lh) and 600 subjects. I batched 600 subjects to run for each label file with the mris_anatomical_stats command. It successfully ran for ~500 subjects. ~60 subjects didnt run at all across all 5 labels. and then there are ~40 subjects that ran for some labels and didnt run for some and I dont really see a pattern. All 100 subjects that didnt run(60 that didnt run at all and 40 that ran for some labels) all had the segmentation error. Thank you for you help! rupa
Can you verify that the label does actually have label points in it? Just open it in a text editor or cat it to a terminal. If it does have points, send it to me. Also let me know which version of FS you are running.
doug
On 3/17/14 5:35 PM, Rupa Sabbineni wrote:
/
/>/ />/ muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l />/ new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh />/ limiting computations to label />/ /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. />/ computing statistics for each annotation in aparc.a2009s.annot. />/ outputting results to outSUB1_lhVOL2... />/ reading volume />/ /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... />/ reading input surface />/ /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... />/ reading input pial surface />/ /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... />/ reading input white surface />/ /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... />/ reading colortable from annotation file... />/ colortable with 76 entries read (originally />/ /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) />/ Segmentation fault: 11 />/ />/ />/ On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni <*MailScanner has detected a possible fraud attempt from "mail.nmr.mgh.harvard.edu" claiming to be* asabbineni at mrn.org https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer />/ <mailto:*MailScanner has detected a possible fraud attempt from "mail.nmr.mgh.harvard.edu" claiming to be* asabbineni at mrn.org https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> wrote: />/ />/ Good morning! />/ />/ />/ I was trying to run the mris_anatomical_stats command and for some />/ subjects I keep getting Segmentation fault:11 error. />/ />/ Some of the posts in the archive suggested that I run the />/ recon-all command since it usually means that subjects surfaces />/ are out of sync SO I RERAN RECON_ALL(which created the stats). />/ Then I reran the mris_anatomical_stats command and got the />/ segmentation fault again. />/ />/ />/ The command im using is />/ />/ mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log />/ outSUB1_lhVOL2 SUB1 lh />/ />/ />/ A little background on the new.label. We got the label by doing a />/ regression in qdec at FDR 0.05 which created cluster and peak />/ cluster label. />/ />/ />/ Can anyone please provide me some insight on how to trouble shoot />/ this problem? />/ />/ Thank you! />/ />/ Rupa />/ />/ />/ />/ />/ -- />/ Rupa />
On Mon, Mar 17, 2014 at 3:35 PM, Rupa Sabbineni <asabbineni@mrn.org mailto:asabbineni@mrn.org> wrote:
muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh limiting computations to label /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. computing statistics for each annotation in aparc.a2009s.annot. outputting results to outSUB1_lhVOL2... reading volume /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... reading input surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading input pial surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... reading input white surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Segmentation fault: 11 On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni <asabbineni@mrn.org <mailto:asabbineni@mrn.org>> wrote: Good morning! I was trying to run the mris_anatomical_stats command and for some subjects I keep getting Segmentation fault:11 error. Some of the posts in the archive suggested that I run the recon-all command since it usually means that subjects surfaces are out of sync SO I RERAN RECON_ALL(which created the stats). Then I reran the mris_anatomical_stats command and got the segmentation fault again. The command im using is mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh A little background on the new.label. We got the label by doing a regression in qdec at FDR 0.05 which created cluster and peak cluster label. Can anyone please provide me some insight on how to trouble shoot this problem? Thank you! Rupa -- Rupa-- Rupa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Doug. I was using the same label file for all subjects before. I will create the labels for each individual and run the mris_anatomical_stats ( I tested it on one subject that didnt run before, and it did not give any errors this time) Thanks again! Rupa
****
It looks like this label was created on fsaverage. Is that the case? If so, then you need to run mri_label2label to map it into the space of an individual, then run mris_anatomical_stats doug
On 03/18/2014 12:59 PM, Rupa Sabbineni wrote:
- Hi Doug*
On Tue, Mar 18, 2014 at 10:59 AM, Rupa Sabbineni asabbineni@mrn.org wrote:
Hi Doug
Attached is a label file.
The FS version is freesurfer-Darwin-lion-stable-pub-v5.3.0
Here's some background information, that might be helpful.
We had 5 label files (2 for rh and 3 for lh) and 600 subjects.
I batched 600 subjects to run for each label file with the mris_anatomical_stats command.
It successfully ran for ~500 subjects. ~60 subjects didnt run at all across all 5 labels. and then there are ~40 subjects that ran for some labels and didnt run for some and I dont really see a pattern. All 100 subjects that didnt run(60 that didnt run at all and 40 that ran for some labels) all had the segmentation error.
Thank you for you help!
rupa
Can you verify that the label does actually have label points in it? Just open it in a text editor or cat it to a terminal. If it does have points, send it to me. Also let me know which version of FS you are running.
doug
On 3/17/14 5:35 PM, Rupa Sabbineni wrote:
- muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l
*>* new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh *>* limiting computations to label *>* /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. *>* computing statistics for each annotation in aparc.a2009s.annot. *>* outputting results to outSUB1_lhVOL2... *>* reading volume *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... *>* reading input surface *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... *>* reading input pial surface *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... *>* reading input white surface *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... *>* reading colortable from annotation file... *>* colortable with 76 entries read (originally *>* /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) *>* Segmentation fault: 11 *>>
- On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni <asabbineni at mrn.org https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
*>* <mailto:asabbineni at mrn.org https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> wrote: *>>* Good morning! *>>>* I was trying to run the mris_anatomical_stats command and for some *>* subjects I keep getting Segmentation fault:11 error. *>>* Some of the posts in the archive suggested that I run the *>* recon-all command since it usually means that subjects surfaces *>* are out of sync SO I RERAN RECON_ALL(which created the stats). *>* Then I reran the mris_anatomical_stats command and got the *>* segmentation fault again. *>>>* The command im using is *>>* mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log *>* outSUB1_lhVOL2 SUB1 lh *>>>* A little background on the new.label. We got the label by doing a *>* regression in qdec at FDR 0.05 which created cluster and peak *>* cluster label. *>>>* Can anyone please provide me some insight on how to trouble shoot *>* this problem? *>>* Thank you! *>>* Rupa *>>>>>* -- *>* Rupa *>
On Mon, Mar 17, 2014 at 3:35 PM, Rupa Sabbineni asabbineni@mrn.orgwrote:
muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh limiting computations to label /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. computing statistics for each annotation in aparc.a2009s.annot. outputting results to outSUB1_lhVOL2... reading volume /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... reading input surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading input pial surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... reading input white surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Segmentation fault: 11
On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni asabbineni@mrn.orgwrote:
Good morning!
I was trying to run the mris_anatomical_stats command and for some subjects I keep getting Segmentation fault:11 error.
Some of the posts in the archive suggested that I run the recon-all command since it usually means that subjects surfaces are out of sync SO I RERAN RECON_ALL(which created the stats). Then I reran the mris_anatomical_stats command and got the segmentation fault again.
The command im using is
mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh
A little background on the new.label. We got the label by doing a regression in qdec at FDR 0.05 which created cluster and peak cluster label.
Can anyone please provide me some insight on how to trouble shoot this problem?
Thank you!
Rupa
-- Rupa
-- Rupa
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Rupa Sabbineni