It could be that there is a problem with one or more of your subjects. First, look at the mask
tksurfer fsaverage_sym lh inflated -overlay mask -fminmax .5 1
the mask should extend over almost all cortex except the medial wall. To look at each subject, you can run
tksurfer fsaverage_sym lh inflated -overlay lh.lh-rh.curv.sm05.mgh -fminmax .1 1 -t lh.lh-rh.curv.sm05.mgh
this will bring up a time course when you click on a point showing all the values for that point. The image you see will be for the first subject, but you can scroll through the subjects using the overlay config window. You may need to adjust the thresholds
doug
On 02/26/2014 09:18 AM, Daniel Carey wrote:
Dear All,
We have been attempting to run a cross hemisphere analysis using .curv files, as per the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
I have outlined the exact steps within our pipeline below. When fitting any glm to the data (simple osgm shown below), we find that across all vertices, the significance values are 0 (despite the vertex by vertex diff values appearing to be very slightly different, based on a cursory inspection of the sig.mgh file overlaid onto lh of fsaverage_sym in tksurfer). Oddly, the vertex by vertex diff values also appear to be lower than we would expect (approximately by a factor of 10). Within the terminal output from glm_fit, we see both F and sig values of 0.
We are unsure as to why the analysis isn't working quite as expected. Any advice on this would be greatly appreciated.
Many thanks in advance,
Dan
# register subs
foreach sub (01 03 04 05 06 08 10 11 12 13 14 15 16 18 19 20 21 22 23 24 25 27 28 29 30 31 32 33 35 36 37 38 39 40)
surfreg --s S$sub-synth --t fsaverage_sym --lh
surfreg --s S$sub-synth --t fsaverage_sym --lh --xhemi
end
# mris_preproc
mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff --srcsurfreg fsaverage_sym.sphere.reg --meas curv --out lh.lh-rh.curv.sm00.mgh \ --s S01-synth --s S03-synth --s S04-synth --s S05-synth --s S06-synth --s S08-synth --s S10-synth --s S11-synth --s S12-synth --s S13-synth --s S14-synth \ --s S15-synth --s S16-synth --s S18-synth --s S19-synth --s S20-synth --s S21-synth --s S22-synth --s S23-synth --s S24-synth --s S25-synth --s S27-synth \ --s S28-synth --s S29-synth --s S30-synth --s S31-synth --s S32-synth --s S33-synth --s S35-synth --s S36-synth --s S37-synth --s S38-synth --s S39-synth \ --s S40-synth
# smooth
mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 5 --i lh.lh-rh.curv.sm00.mgh --o lh.lh-rh.curv.sm05.mgh
# mris_glmfit
mri_glmfit --y lh.lh-rh.curv.sm05.mgh --glmdir glm.lh.lh-rh.curv.sm05.osgm --osgm --surf fsaverage_sym lh
Daniel Carey Marie Curie Ph.D. Fellow, Centre for Brain and Cognitive Development, 32 Torrington Sq., London WC1E 7HX UK
email: d.carey@bbk.ac.uk mailto:d.carey@bbk.ac.uk web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey
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