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.ca...@bbk.ac.uk <mailto:d.ca...@bbk.ac.uk> > web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
