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 <[email protected]>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 < >> [email protected] >> <mailto:[email protected].**edu<[email protected]>>> >> 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 >> <[email protected] >> <mailto:[email protected].**edu<[email protected]> >> > >> <mailto:[email protected].**edu <[email protected]> >> <mailto:[email protected].**edu <[email protected]>>>> >> 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 >> <[email protected] >> <mailto:[email protected].**edu <[email protected]>> >> <mailto:[email protected].**edu <[email protected]> >> <mailto:[email protected].**edu <[email protected]>>> >> >> <mailto:[email protected].**edu<[email protected]> >> <mailto:[email protected].**edu <[email protected]>> >> >> >> <mailto:[email protected].**edu<[email protected]> >> <mailto:[email protected].**edu <[email protected]>>>>> >> 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 >> > [email protected] >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> > >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> > >> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >>> >> >> > >> >> 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 >> [email protected] >> <mailto:[email protected].**edu<[email protected]> >> > >> <mailto:[email protected].**edu <[email protected]> >> <mailto:[email protected].**edu <[email protected]>>> >> >> <mailto:[email protected].**edu<[email protected]> >> <mailto:[email protected].**edu <[email protected]>> >> >> >> <mailto:[email protected].**edu<[email protected]> >> <mailto:[email protected].**edu <[email protected]> >> >>> >> >> 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.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> >> > >> <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 >> [email protected] >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> > >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> > >> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >> <mailto:[email protected].**harvard.edu<[email protected]> >> >>> >> >> >> 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 >> [email protected] >> <mailto:[email protected].**edu<[email protected]> >> > >> <mailto:[email protected].**edu <[email protected]> >> <mailto:[email protected].**edu <[email protected]>>> >> 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 >> [email protected] >> <mailto:[email protected].**edu<[email protected]> >> > >> 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 > [email protected] > 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<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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >
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