that makes sense. also just for clarification to a point a made before - i was not using label2label to transfer the rh.cortex.label we have been discussing across subjects, i was transferring other labels, which is most likely why the label2label and measurements didnt fail. I believe i misunderstood the rh.cortex.label's use, i was under the impression it was necessary to create the subjects inflated surface and measure thickness, but it appears i was wrong . Sorry for any confusion on that point, it was due to my poor wording of the situation.
best- michael On Fri, Jun 1, 2012 at 12:25 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > not unless you are trying to visualize the label > > > On 06/01/2012 01:16 PM, mdkrue...@uwalumni.com wrote: > >> Thanks, i am also still able to display the rh in tksurfer without issue, >> shouldnt that also fail with the current rh.cortex.label? >> >> michael >> >> On Fri, Jun 1, 2012 at 11:57 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >> wrote: >> >> I would have expected that to fail. You can check the time stamps >> to see >> if your output is newer or older than rh.cortex.label. If older, it is >> probably ok. >> >> On 06/01/2012 12:53 PM, mdkrue...@uwalumni.com >> <mailto:mdkrue...@uwalumni.com**> wrote: >> > Actually one last question- >> > >> > I used label2label to transfer some labels and grab ROI thickness >> > averages from the labels on the subject with the rh.cortex.label >> that >> > has been overwritten. I received no errors during this, does >> this mean >> > that the label transfers and averages are valid, or do i need to >> redo >> > them? >> > >> > Best- >> > Michael >> > >> > >> > >> > On Fri, Jun 1, 2012 at 11:05 AM, mdkrue...@uwalumni.com >> <mailto:mdkrue...@uwalumni.com**> >> > <mailto:mdkrue...@uwalumni.com <mailto:mdkrue...@uwalumni.com**>> >> <mdkrue...@uwalumni.com <mailto:mdkrue...@uwalumni.com**> >> > <mailto:mdkrue...@uwalumni.com <mailto:mdkrue...@uwalumni.com**>>> >> >> wrote: >> > >> > Doug - >> > >> > That does indeed seem to be the problem! Ill just rerun some >> > things here to rectify that. Thanks for all the help >> everyone! >> > >> > Best- >> > Michael >> > >> > On Fri, Jun 1, 2012 at 11:01 AM, Douglas N Greve >> > <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu><mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>>> >> >> > wrote: >> > >> > I think the label file got overwritten at some point. >> > Check the time >> > stamp and see if it is much different than the other >> rh files >> > >> > On 06/01/2012 11:55 AM, mdkrue...@uwalumni.com >> <mailto:mdkrue...@uwalumni.com**> >> > <mailto:mdkrue...@uwalumni.com <mailto:mdkrue...@uwalumni.com**>> >> >> wrote: >> > > Bruce- >> > > >> > > It is, and i agree, for instance here is the >> > lh.cortex.label file >> > > >> > > #label , from subject ?? >> > > 149955 >> > > 22 -10.374 55.016 3.203 0.0000000000 >> > > 112 -6.294 36.386 -7.809 0.0000000000 >> > > 114 -6.137 38.556 13.808 0.0000000000 >> > > 247 -11.304 45.214 -2.709 0.0000000000 >> > > 248 -6.278 39.973 2.192 0.0000000000 >> > > 249 -10.766 45.545 6.476 0.0000000000 >> > > 507 -11.087 42.990 18.865 0.0000000000 >> > > >> > > On 6/1/12, Bruce >> Fischl<fis...@nmr.mgh.harvard.**edu<fis...@nmr.mgh.harvard.edu> >> <mailto:fis...@nmr.mgh.**harvard.edu <fis...@nmr.mgh.harvard.edu>> >> > <mailto:fis...@nmr.mgh.**harvard.edu <fis...@nmr.mgh.harvard.edu> >> >> <mailto:fis...@nmr.mgh.**harvard.edu <fis...@nmr.mgh.harvard.edu>>>> >> wrote: >> > >> that is the rh.cortex.label file? It doesn't look like >> > it.... >> > >> >> > >> On Fri, 1 Jun 2012, mdkrue...@uwalumni.com >> <mailto:mdkrue...@uwalumni.com**> >> > <mailto:mdkrue...@uwalumni.com <mailto:mdkrue...@uwalumni.com**>> >> >> > >> wrote: >> > >> >> > >>> Bruce- >> > >>> >> > >>> Here you go. Subjects recoded. >> > >>> >> > >>> Graph: name >> > >>> >> > >>> Data: path >> > >>> Variable: Subject >> > >>> Measurement: external >> > >>> subject id, class id, variable value, measurement >> > value, standard >> > >>> deviation >> > >>> ------------ >> > >>> S1 Cl1 0.0 3.10522500831 0.268702566292 >> > >>> S2 Cl1 1.0 2.67585065105 0.396833961125 >> > >>> S3 Cl1 2.0 3.07631433273 0.173949345568 >> > >>> S4 Cl1 3.0 2.85668014067 0.0907729539181 >> > >>> S5 Cl1 4.0 3.24184323479 0.212597547853 >> > >>> S6 Cl1 5.0 2.54176559894 0.111183384791 >> > >>> S7 Cl1 6.0 2.87165045086 0.137271513295 >> > >>> S8 Cl1 7.0 2.72165358457 0.128648203321 >> > >>> >> > >>> On 6/1/12, Bruce >> Fischl<fis...@nmr.mgh.harvard.**edu<fis...@nmr.mgh.harvard.edu> >> <mailto:fis...@nmr.mgh.**harvard.edu <fis...@nmr.mgh.harvard.edu>> >> > <mailto:fis...@nmr.mgh.**harvard.edu <fis...@nmr.mgh.harvard.edu> >> >> <mailto:fis...@nmr.mgh.**harvard.edu <fis...@nmr.mgh.harvard.edu>>>> >> wrote: >> > >>>> something like this: >> > >>>> >> > >>>> head ~/local_subjects/bruce/label/**rh.cortex.label >> > >>>> #!ascii label , from subject vox2ras=TkReg >> > >>>> 141813 >> > >>>> 0 11.129 -93.761 -16.820 0.0000000000 >> > >>>> 1 11.136 -93.912 -16.623 0.0000000000 >> > >>>> 2 10.755 -93.913 -16.573 0.0000000000 >> > >>>> 3 11.696 -93.374 -17.237 0.0000000000 >> > >>>> 4 11.022 -93.203 -16.969 0.0000000000 >> > >>>> 5 11.020 -93.855 -17.042 0.0000000000 >> > >>>> 6 10.248 -93.745 -16.712 0.0000000000 >> > >>>> 7 11.591 -93.603 -17.551 0.0000000000 >> > >>>> >> > >>>> >> > >>>> >> > >>>> and please cc the list so others can answer! >> > >>>> On Fri, 1 Jun 2012, >> > >>>> mdkrue...@uwalumni.com <mailto:mdkrue...@uwalumni.com**> >> > <mailto:mdkrue...@uwalumni.com <mailto:mdkrue...@uwalumni.com**>> >> >> wrote: >> > >>>> >> > >>>>> Bruce- >> > >>>>> The partition does not appear to be full, although >> > we have been having >> > >>>>> issues with migrating data so >> > >>>>> that could be a source of the issue. The >> > rh.cortex.label does exist and >> > >>>>> is >> > >>>>> located within the subject's >> > >>>>> label dir. As for the first couple of lines, I am >> > unsure what you are >> > >>>>> asking for. >> > >>>>> >> > >>>>> Thanks for the quick response! >> > >>>>> >> > >>>>> Best- >> > >>>>> Michael >> > >>>>> >> > >>>>> On Fri, Jun 1, 2012 at 10:26 AM, Bruce Fischl >> > >>>>> <fis...@nmr.mgh.harvard.edu >> <mailto:fis...@nmr.mgh.**harvard.edu <fis...@nmr.mgh.harvard.edu>> >> > <mailto:fis...@nmr.mgh.**harvard.edu <fis...@nmr.mgh.harvard.edu> >> >> <mailto:fis...@nmr.mgh.**harvard.edu <fis...@nmr.mgh.harvard.edu>>>> >> > >>>>> wrote: >> > >>>>> Hi Michael >> > >>>>> >> > >>>>> can you check to see that your partition is >> > not full? Does the >> > >>>>> rh.cortex.label file exist >> > >>>>> in that subject's label dir? If so, what are >> > the first couple of >> > >>>>> lines? >> > >>>>> >> > >>>>> cheers >> > >>>>> Bruce >> > >>>>> >> > >>>>> On Fri, 1 Jun 2012, mdkrue...@uwalumni.com >> <mailto:mdkrue...@uwalumni.com**> >> > <mailto:mdkrue...@uwalumni.com <mailto:mdkrue...@uwalumni.com**>> >> >> wrote: >> > >>>>> >> > >>>>> To anyone who can help - >> > >>>>> I am trying to tun a GLM on a set of >> > data and am currently >> > >>>>> receiving an error >> > >>>>> during the mri_surf2surf >> > >>>>> portion. When running this portion i >> > receive an error ( >> > >>>>> could >> > >>>>> not scan # of >> > >>>>> lines from (path to >> > >>>>> rh.cortex.label)). This does not happen >> > when running this >> > >>>>> portion for the lh, >> > >>>>> only the right. I am >> > >>>>> unable to find any information on this >> > error on the mailing >> > >>>>> list so im hoping >> > >>>>> someone can help! >> > >>>>> >> > >>>>> Best- >> > >>>>> Michael Kruepke >> > >>>>> >> > >>>>> -- >> > >>>>> Michael D. Kruepke >> > >>>>> PhD - University of Illinois at >> > Urbana-Champaign >> > >>>>> BA - Psych - University of >> > Wisconsin-Madison >> > >>>>> mdkrue...@gmail.com <mailto:mdkrue...@gmail.com> >> <mailto:mdkrue...@gmail.com <mailto:mdkrue...@gmail.com>> >> >> > >>>>> (262)-483-7449 <tel:%28262%29-483-7449> >> <tel:%28262%29-483-7449> >> > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> 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. >> > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> -- >> > >>>>> Michael D. Kruepke >> > >>>>> PhD - University of Illinois at Urbana-Champaign >> > >>>>> BA - Psych - University of Wisconsin-Madison >> > >>>>> mdkrue...@gmail.com <mailto:mdkrue...@gmail.com> >> <mailto:mdkrue...@gmail.com <mailto:mdkrue...@gmail.com>> >> > >>>>> (262)-483-7449 <tel:%28262%29-483-7449> >> >> <tel:%28262%29-483-7449> >> > >>>>> >> > >>>>> >> > >>>>> >> > >>> >> > >>> >> > > >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu><mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> > Fax: 617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 <tel: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: >> > >> 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> >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> > <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@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> >> > >> > >> > >> > >> > -- >> > Michael D. Kruepke >> > PhD - University of Illinois at Urbana-Champaign >> > BA - Psych - University of Wisconsin-Madison >> > mdkrue...@gmail.com <mailto:mdkrue...@gmail.com> >> <mailto:mdkrue...@gmail.com <mailto:mdkrue...@gmail.com>> >> > (262)-483-7449 <tel:%28262%29-483-7449> <tel:%28262%29-483-7449> >> >> > >> > >> > >> > >> > -- >> > Michael D. Kruepke >> > PhD - University of Illinois at Urbana-Champaign >> > BA - Psych - University of Wisconsin-Madison >> > mdkrue...@gmail.com <mailto:mdkrue...@gmail.com> >> <mailto:mdkrue...@gmail.com <mailto:mdkrue...@gmail.com>> >> > (262)-483-7449 <tel:%28262%29-483-7449> <tel:%28262%29-483-7449> >> >> > >> > >> > >> > >> > -- >> > Michael D. Kruepke >> > PhD - University of Illinois at Urbana-Champaign >> > BA - Psych - University of Wisconsin-Madison >> > mdkrue...@gmail.com <mailto:mdkrue...@gmail.com> >> <mailto:mdkrue...@gmail.com <mailto:mdkrue...@gmail.com>> >> > (262)-483-7449 <tel:%28262%29-483-7449> >> > >> > >> > >> >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:freesur...@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 >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel: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: >> 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> >> > >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@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> >> >> >> >> >> -- >> Michael D. Kruepke >> PhD - University of Illinois at Urbana-Champaign >> BA - Psych - University of Wisconsin-Madison >> mdkrue...@gmail.com <mailto:mdkrue...@gmail.com> >> (262)-483-7449 >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkrue...@gmail.com (262)-483-7449
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