I've added a voxel-based analysis to the wiki page https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
Note that I'm recommending using permutation instead of GRF for correction of multiple comparisons
On 08/29/2017 10:03 AM, John Anderson wrote:
Hi Dr Greve,
I am using pet surfer to analyze suv images. I followed all the steps in wiki, I used the option mgx then I fed the imagesmgx.{ctxgm,subctxgm,gm} into surface based analysis for left and right hemispheres. I want to inquire about the sub cortical analysis.
- I assume the analysis for sub cortical gray matter (i.e. using the
imagessubctxgm) is volumetric. Is this correct?
Yes. This is on the wiki page.
- Are the following steps correct for sub cortical gray matter analysis
mri_vol2vol --movsubctxgm.nii.gz --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --osubctxgm.tal2mm.nii.gz
mri_masksubctxgm.tal2mm.nii.gz $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgzsubctxgm.tal2mm_subc.nii.gz &
Concatenate all subjects together using mri_concat
smooth using mri_fwhm (what is the recommended smoothing for suv)?
Then Group analysis:
mri_glmfit --y all.suvr.tal2mm.subc.sm10.nii --fsgd fsgd.dat --C contrast.mtx --glmdir dir
mri_glmfit-sim --glmdir dir --grf 1.3 pos --cwpvalthresh 0.0166
for "mri_glmfit-sim" in subcortical structure is the flag grf correct or cache?
Thanks in advance! John
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