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 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/