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