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 > <[email protected] <mailto:[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]> > <mailto:[email protected] > <mailto:[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]> > <mailto:[email protected] > <mailto:[email protected]>> > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[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]> > <mailto:[email protected] > <mailto:[email protected]>> > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>> > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[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]> > <mailto:[email protected] > <mailto:[email protected]>> > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>> > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>> > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[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> > 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 > [email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>> > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>>> > > 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 > [email protected] <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[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 > 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 > [email protected] <mailto:[email protected]> > <mailto:[email protected] > <mailto:[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> > 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 > [email protected] <mailto:[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 > 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 [email protected] 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/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
