This time, selxavg3-sess finished without any error but everything outside the brain including eyes are cut (for me i.e. failure). Apparently, no-mask flag is ignored (!). To help you find the problem I copy/paste my commands here:
preproc-sess -s Sbj_53/abir/ -fwhm 2 -per-session -fsd bold -no-subcort-mask mkanalysis-sess -analysis RetinaPrj_New -fwhm 2 -paradigm Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -runlistfile RunList -per-session -fsd bold -no-subcort-mask -no-mask selxavg3-sess -s Sbj_53/abir -a RetinaPrj_New I am also attaching the analysis.info If you want to test the files, you can see the subject files in: /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir Note: I did all of these tests from scratch after deleting files from the previous tests. So it can't be due to a remaining file from the previous processes. On Thu, Oct 3, 2013 at 3:47 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > OK, try it like this using the dev env > 1. When you run preproc-sess use -no-subcort-mask but do not spec -nomask > 2. When ruy run mkanalysis-sess use both -no-subcort-mask and -no-mask > > Note that the eyes may get cut off in the mni305 space. You might just > want to keep it in native space. > > doug > > > > > > > On 10/03/2013 03:19 PM, sha...@nmr.mgh.harvard.edu wrote: > >> 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 <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<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: >>>> 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/> >>>> > >>>> > >>>> > >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> 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<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/> >>> >>> >>> >>> >> > -- > 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: > 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/> > > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
analysis.info
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