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>> 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.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
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/
--
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/