28 May
2013
28 May
'13
11:06 a.m.
Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug
On 05/28/2013 10:33 AM, Rob Tennyson wrote:
Hi Doug,
Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well.
I am also going to review the white surface soon as Bruce suggested.
On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: > Hi All, > > I'm running "mris_anatomical_stats" with a few manually defined > labels. For a few of my subjects, I am getting the error: > "Segmentation fault" on one of the labels. However, the other manually > defined labels process without any errors on these same subjects. > > For example, I am running "mri_anatomical_stats" on subject 33_bay6 > with a manually defined ERC label, a manually defined PHC label, and a > manually defined medial frontal gyrus label. The only label that runs > an error for this subject is the PHC label. This PHC label runs > without any errors on the rest of my subjects. > > Here is what is displayed when running a label that fails: > > "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b > 33_bay6 lh > limiting computations to label lh.PHC_1.label. > reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... > reading input surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... > reading input pial surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... > reading input white surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... > Segmentation fault" > > Does anyone know what may be causing the Segmentation fault and what > steps I should take to fix it? > > Thank you for your help! > Rob > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
28 May
28 May
2:32 p.m.
New subject: mri_anatomical_stats segmentation fault
Hi Doug,
It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label.
Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look?
Thanks! Rob
On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug
On 05/28/2013 10:33 AM, Rob Tennyson wrote:
Hi Doug,
Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well.
I am also going to review the white surface soon as Bruce suggested.
On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: > Hi All, > > I'm running "mris_anatomical_stats" with a few manually defined > labels. For a few of my subjects, I am getting the error: > "Segmentation fault" on one of the labels. However, the other manually > defined labels process without any errors on these same subjects. > > For example, I am running "mri_anatomical_stats" on subject 33_bay6 > with a manually defined ERC label, a manually defined PHC label, and a > manually defined medial frontal gyrus label. The only label that runs > an error for this subject is the PHC label. This PHC label runs > without any errors on the rest of my subjects. > > Here is what is displayed when running a label that fails: > > "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b > 33_bay6 lh > limiting computations to label lh.PHC_1.label. > reading volume /Volumes/BigRaid/Rob/subjects/**33_bay6/mri/wm.mgz... > reading input surface > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white... > reading input pial surface > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.pial... > reading input white surface > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white... > Segmentation fault" > > Does anyone know what may be causing the Segmentation fault and what > steps I should take to fix it? > > Thank you for your help! > Rob > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
2:52 p.m.
New subject: mri_anatomical_stats segmentation fault
how did you create the label? If it has more vertices than the subject has then something is very wrong. You don't always get segfaults, you might just get garbage and never know it. doug
On 05/28/2013 02:32 PM, Rob Tennyson wrote:
Hi Doug,
It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label.
Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look?
Thanks! Rob
On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: > Hi All, > > I'm running "mris_anatomical_stats" with a few manually defined > labels. For a few of my subjects, I am getting the error: > "Segmentation fault" on one of the labels. However, the other manually > defined labels process without any errors on these same subjects. > > For example, I am running "mri_anatomical_stats" on subject 33_bay6 > with a manually defined ERC label, a manually defined PHC label, and a > manually defined medial frontal gyrus label. The only label that runs > an error for this subject is the PHC label. This PHC label runs > without any errors on the rest of my subjects. > > Here is what is displayed when running a label that fails: > > "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b > 33_bay6 lh > limiting computations to label lh.PHC_1.label. > reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... > reading input surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... > reading input pial surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... > reading input white surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... > Segmentation fault" > > Does anyone know what may be causing the Segmentation fault and what > steps I should take to fix it? > > Thank you for your help! > Rob > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
3 p.m.
New subject: mri_anatomical_stats segmentation fault
The labels are built from areas that showed between-group functional differences. I am able to view the label on the subject in question in freeview.
Maybe I'm looking at the wrong place in the output of mris_info? Or perhaps in the wrong file. I looked at "nvertices" in our "lh.white" file.
On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
how did you create the label? If it has more vertices than the subject has then something is very wrong. You don't always get segfaults, you might just get garbage and never know it. doug
On 05/28/2013 02:32 PM, Rob Tennyson wrote:
Hi Doug,
It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label.
Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look?
Thanks! Rob
On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>wrote:
Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: > Hi All, > > I'm running "mris_anatomical_stats" with a few manually defined > labels. For a few of my subjects, I am getting the error: > "Segmentation fault" on one of the labels. However, the other manually > defined labels process without any errors on these same subjects. > > For example, I am running "mri_anatomical_stats" on subject 33_bay6 > with a manually defined ERC label, a manually defined PHC label, and a > manually defined medial frontal gyrus label. The only label that runs > an error for this subject is the PHC label. This PHC label runs > without any errors on the rest of my subjects. > > Here is what is displayed when running a label that fails: > > "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b > 33_bay6 lh > limiting computations to label lh.PHC_1.label. > reading volume /Volumes/BigRaid/Rob/subjects/**33_bay6/mri/wm.mgz... > reading input surface > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white... > reading input pial surface > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.pial... > reading input white surface > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white... > Segmentation fault" > > Does anyone know what may be causing the Segmentation fault and what > steps I should take to fix it? > > Thank you for your help! > Rob > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html><http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
3:06 p.m.
New subject: mri_anatomical_stats segmentation fault
The label that you sent applies to fsaverage. If you want to use it on a different subject, you should map it to that subject with mri_label2label doug
On 05/28/2013 03:00 PM, Rob Tennyson wrote:
The labels are built from areas that showed between-group functional differences. I am able to view the label on the subject in question in freeview.
Maybe I'm looking at the wrong place in the output of mris_info? Or perhaps in the wrong file. I looked at "nvertices" in our "lh.white" file.
On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
how did you create the label? If it has more vertices than the subject has then something is very wrong. You don't always get segfaults, you might just get garbage and never know it. doug On 05/28/2013 02:32 PM, Rob Tennyson wrote: Hi Doug, It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label. Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look? Thanks! Rob On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: > Hi All, > > I'm running "mris_anatomical_stats" with a few manually defined > labels. For a few of my subjects, I am getting the error: > "Segmentation fault" on one of the labels. However, the other manually > defined labels process without any errors on these same subjects. > > For example, I am running "mri_anatomical_stats" on subject 33_bay6 > with a manually defined ERC label, a manually defined PHC label, and a > manually defined medial frontal gyrus label. The only label that runs > an error for this subject is the PHC label. This PHC label runs > without any errors on the rest of my subjects. > > Here is what is displayed when running a label that fails: > > "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b > 33_bay6 lh > limiting computations to label lh.PHC_1.label. > reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... > reading input surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... > reading input pial surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... > reading input white surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... > Segmentation fault" > > Does anyone know what may be causing the Segmentation fault and what > steps I should take to fix it? > > Thank you for your help! > Rob > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
3:15 p.m.
New subject: mri_anatomical_stats segmentation fault
That explains a lot about my problem subjects.
Just to confirm, I should use mri_label2label with fsaverage as the source subject and the subject in question as the target? Having this run for all of my subjects will then allow me to use mris_anatomical_stats for each subject.
Thanks for the help!
On Tue, May 28, 2013 at 2:06 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
The label that you sent applies to fsaverage. If you want to use it on a different subject, you should map it to that subject with mri_label2label doug
On 05/28/2013 03:00 PM, Rob Tennyson wrote:
The labels are built from areas that showed between-group functional differences. I am able to view the label on the subject in question in freeview.
Maybe I'm looking at the wrong place in the output of mris_info? Or perhaps in the wrong file. I looked at "nvertices" in our "lh.white" file.
On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
how did you create the label? If it has more vertices than the subject has then something is very wrong. You don't always get segfaults, you might just get garbage and never know it. doug On 05/28/2013 02:32 PM, Rob Tennyson wrote: Hi Doug, It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label. Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look? Thanks! Rob On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>wrote:
Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>>wrote:
Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: > Hi All, > > I'm running "mris_anatomical_stats" with a few manually defined > labels. For a few of my subjects, I am getting the error: > "Segmentation fault" on one of the labels. However, the other manually > defined labels process without any errors on these same subjects. > > For example, I am running "mri_anatomical_stats" on subject 33_bay6 > with a manually defined ERC label, a manually defined PHC label, and a > manually defined medial frontal gyrus label. The only label that runs > an error for this subject is the PHC label. This PHC label runs > without any errors on the rest of my subjects. > > Here is what is displayed when running a label that fails: > > "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b > 33_bay6 lh > limiting computations to label lh.PHC_1.label. > reading volume /Volumes/BigRaid/Rob/subjects/**33_bay6/mri/wm.mgz... > reading input surface > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white... > reading input pial surface > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.pial... > reading input white surface > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white... > Segmentation fault" > > Does anyone know what may be causing the Segmentation fault and what > steps I should take to fix it? > > Thank you for your help! > Rob > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.** edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html><http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
3:33 p.m.
New subject: mri_anatomical_stats segmentation fault
yes On 05/28/2013 03:15 PM, Rob Tennyson wrote:
That explains a lot about my problem subjects.
Just to confirm, I should use mri_label2label with fsaverage as the source subject and the subject in question as the target? Having this run for all of my subjects will then allow me to use mris_anatomical_stats for each subject.
Thanks for the help!
On Tue, May 28, 2013 at 2:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The label that you sent applies to fsaverage. If you want to use it on a different subject, you should map it to that subject with mri_label2label doug On 05/28/2013 03:00 PM, Rob Tennyson wrote: The labels are built from areas that showed between-group functional differences. I am able to view the label on the subject in question in freeview. Maybe I'm looking at the wrong place in the output of mris_info? Or perhaps in the wrong file. I looked at "nvertices" in our "lh.white" file. On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: how did you create the label? If it has more vertices than the subject has then something is very wrong. You don't always get segfaults, you might just get garbage and never know it. doug On 05/28/2013 02:32 PM, Rob Tennyson wrote: Hi Doug, It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label. Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look? Thanks! Rob On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: > Hi All, > > I'm running "mris_anatomical_stats" with a few manually defined > labels. For a few of my subjects, I am getting the error: > "Segmentation fault" on one of the labels. However, the other manually > defined labels process without any errors on these same subjects. > > For example, I am running "mri_anatomical_stats" on subject 33_bay6 > with a manually defined ERC label, a manually defined PHC label, and a > manually defined medial frontal gyrus label. The only label that runs > an error for this subject is the PHC label. This PHC label runs > without any errors on the rest of my subjects. > > Here is what is displayed when running a label that fails: > > "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b > 33_bay6 lh > limiting computations to label lh.PHC_1.label. > reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... > reading input surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... > reading input pial surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... > reading input white surface > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... > Segmentation fault" > > Does anyone know what may be causing the Segmentation fault and what > steps I should take to fix it? > > Thank you for your help! > Rob > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Rob Tennyson