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 greve@nmr.mgh.harvard.eduwrote:

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, shahin@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, <shahin@nmr.mgh.harvard.edu <mailto:shahin@nmr.mgh.**harvard.edu shahin@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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/