Hi Doug and Freesurfers, No matter what I try I am still getting the Dimension mismatch error when running fieldsign-sess. I even ran recon-all -s sj12 -make all.
I don't think it's a problem with the directories (below). The subjectname file is correct, and when I run field-sign-sess it sees the anatomical directory. What else do you recommend? Thanks. Michelle On Mon, Oct 3, 2011 at 4:36 PM, Michelle Umali <mumal...@gmail.com> wrote: > Hi Doug, > I keep my retinotopy (sj) and anatomical (ld) data separate. I named the > retinotopy directory sj12 with the subjectname file says ld12, which is the > anatomical directory for the same subject. > > -Michelle > > > On Mon, Oct 3, 2011 at 4:31 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > > wrote: > >> Can you check that the subjectname file is correct? In some cases, it >> looks like it is using subject sj12, in others it looks like it is using >> subject ld12. >> doug >> >> Michelle Umali wrote: >> >>> Hi Doug, >>> >>> I re-ran from preproc-sess using the -force flag, and I still get the >>> same dimension mismatch error. >>> >>> I'm attaching the terminal output starting from pre-proc-sess. >>> >>> What's the next step? >>> >>> Thanks. >>> Michelle >>> >>> On Mon, Oct 3, 2011 at 3:23 PM, Douglas N Greve < >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >>> wrote: >>> >>> You can an asynchrony between your fmri data and the anatomical: >>> Anatomical: num vertices: 146530 >>> fMRI: 158944 vertices >>> >>> re-run the fMRI starting from preproc-sess. You will need to make >>> sure that preproc-sess actually re-runs at least the >>> sample-to-surface. By default, it just looks to see if things are >>> up-to-date (but does not check the anatomical). So, you can run it >>> with -force. This will cause it to re-run everything. Or you can >>> delete the surface files in the bold directories and re-run >>> without -force. >>> >>> doug >>> >>> >>> >>> Michelle Umali wrote: >>> >>> Hi Doug, >>> >>> I've attached the mri_info output on the eccen and polar >>> images as well as the mris_info on the lh.sphere surface >>> >>> Thanks. >>> Michelle >>> >>> On Mon, Oct 3, 2011 at 2:38 PM, 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: >>> >>> Can you send me the result of running mri_info on >>> eccen/real.nii >>> eccen/imag.nii >>> polar/real.nii >>> polar/imag.nii >>> in the >>> /usr/local/freesurfer/**subjects/retinotopy/sj12/bold/* >>> *rtopy.self.lh >>> directory? >>> >>> And the result of >>> mris_info >>> /usr/local/freesurfer/**subjects/retinotopy/sj12/surf/** >>> lh.sphere >>> >>> doug >>> >>> >>> >>> >>> >>> Michelle Umali wrote: >>> >>> Hi Doug, >>> I've attached the output from running fieldsign-sess. >>> >>> Thanks for all your help. >>> Michelle >>> >>> On Mon, Oct 3, 2011 at 12:59 PM, 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>>> >>> <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> >>> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>>>> >>> wrote: >>> >>> Michelle, before you do that, can you run the >>> offending program >>> with -debug and send me the (copious) terminal >>> output? Your >>> anat >>> should not have to be re-run. >>> >>> doug >>> >>> Michelle Umali wrote: >>> >>> Hi Bruce, >>> Will this undo my wm and pial edits? >>> >>> Thanks. >>> Michelle >>> >>> On Sat, Oct 1, 2011 at 3:37 PM, 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> >>> >> >>> >>> <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> >>> <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> >>> > >>> >>> <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> >>> <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: >>> >>> try running >>> >>> >>> recon-all -s subject -make all >>> >>> and leave the -dontrun off. It should bring >>> everything up >>> to date >>> >>> Bruce >>> >>> >>> >>> On Sat, 1 Oct 2011, Michelle Umali wrote: >>> >>> Dear Freesurfers, >>> I'm still getting a MRISripZeros() and >>> MRIScopyMRI Surf/src >>> mismatch error >>> when running fieldsign-sess. You >>> suggested that >>> this >>> problem >>> was due to the >>> surfaces being out of synch. When I ran >>> recon-all -s >>> subject >>> -make all >>> -dontrun, I saw that several steps had >>> not run. >>> The data >>> looked alright and >>> the number of vertices matched when I ran >>> -vno-check. >>> >>> The mismatch error is still occurring, and I >>> don't know >>> how to >>> proceed. >>> >>> Please suggest steps that I should take. >>> >>> Thanks. >>> Michelle >>> >>> >>> >>> >>> >>> 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. >>> >>> >>> ------------------------------** >>> ------------------------------**------------ >>> >>> >>> >>> ______________________________**_________________ >>> 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> >>> >> >>> >>> <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> >>> >>> <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>> >>> <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> >>> <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>> >>> <tel: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>> >>> <tel: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> >>> > >>> <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> >>> > >>> <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> >>> >>> >>> -- 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> >>> > >>> >>> 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 >>> 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 >> 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> >> >> >
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