Hi Doug,
Thanks for the response. Is this masking out of the cortical regions in the
volume analysis a newer aspect of the processing stream? Previously I have seen
this activation in the volume.
It would be great if you could let me know the flags to see the full volume
analysis.
Thanks!
Emily
Message: 41
Date: Wed, 07 Aug 2013 19:29:33 -0400
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Different results in surface and volume
analyses
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5202d85d.1090...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Emily, the processing stream is designed to mask out cortical regions
from the volume analysis. The volume analysis is used for subcortical
structures. To make sure that the same voxels are not analyzed twice,
the cortical surface is masked out of the mni305 analysis.
doug
ps. If you really want to see the full volume analysis, then there are
some flags that will do this.
Message: 14
Date: Wed, 7 Aug 2013 13:15:37 -0400
From: Emily Boeke <eboek...@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Different results in surface and volume analyses
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <948e8fdf-754a-4ae0-a0c9-86d848f14...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=us-ascii
Hello everyone,
I am looking at a visual stimulus vs fixation contrast in my individual
subjects' data to make sure we are seeing normal activation there. If I look at
the surface data in tksurfer, I see activation in the occipital cortex, but in
the mni305 analysis, there is no activation in this region.
These are the preprocess , mkanalysis, and selxavg commands I used for the
surface vs. mni305:
preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down -surface
fsaverage lhrh -mni305-2mm -fsd cond
mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm
Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0
-refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down
mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm
Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0
-refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down
mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par
-event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6
-analysis cond.sm05.mni305 -per-run -nskip 4 -stc down
selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh
selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh
selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305
Why might we be seeing this activation on the surface map but not the volume
one?
Thanks!
Emily
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