preproc-sess -s <SbjName> -fwhm 2 -per-run -fsd bold -mni305-1mm -nomask -no-subcort-mask
I also tried per-session and mni305-2mm but still did not help. I even tried doing it in native space (by not mentioning mni305/fsaverage) but did not work either. > What was your preproc-sess command? > > > On 10/03/2013 10:29 AM, SHAHIN NASR wrote: >> Hi Doug, >> Did you have a chance to find the reason for this problem? >> >> >> On Wed, Oct 2, 2013 at 3:20 PM, <sha...@nmr.mgh.harvard.edu >> <mailto:sha...@nmr.mgh.harvard.edu>> wrote: >> >> I still receive the same error message (1mm is now 2mm in the >> message). >> >> outanadir = >> >> /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask2 >> Error using MRIread (line 76) >> ERROR: cannot determine format of >> >> /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/008/masks/.mni305.2mm >> (MRIread) >> >> >> Error in fast_selxavg3 (line 146) >> runmask = MRIread(flac.maskfspec); >> >> >> >> > Does the same thing happen if you use the 2mm instead of the 1mm? >> > >> > On 10/02/2013 02:21 PM, SHAHIN NASR wrote: >> >> Hi, >> >> I want to test activity outside the brain (around >> eyes/retina) but >> >> when I use "-no-mask" flag in my mkanalysis-sess (to be able to >> see >> >> activity outside brain) as below: >> >> >> >> mkanalysis-sess -analysis RetinaPrj_nomask -fwhm 2 -paradigm >> >> Conds.par -mni305 1 -event-related -polyfit 2 -gammafit 2.25 1.25 >> >> -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -force >> -runlistfile >> >> RunList -per-run -fsd bold -no-mask >> >> >> >> I get this error: >> >> >> >> outanadir = >> >> >> >> /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask >> >> Error using MRIread (line 76) >> >> ERROR: cannot determine format of >> >> >> >> /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/008/masks/.mni305.1mm >> >> (MRIread) >> >> >> >> >> >> Error in fast_selxavg3 (line 146) >> >> runmask = MRIread(flac.maskfspec); >> >> >> ------------------------------------------ >> >> ERROR: fast_selxavg3() failed\n >> >> >> >> Note: >> >> ** I have already used -nomask and -no-subcort-mask in the >> preproc-sess >> >> *** If I remove this flag, everything looks fine except for the >> fact >> >> that all activity outside brain is masked! >> >> >> >> >> >> -- >> >> Shahin Nasr >> >> >> >> PhD in Cognitive Neuroscience >> >> Martinos Imaging Center, MGH >> >> Harvard Medical School >> >> >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > gr...@nmr.mgh.harvard.edu <mailto: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> >> > 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/ >> > >> > >> > >> >> >> >> >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School > > -- > 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 > 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 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.
