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 images mgx.{ctxgm,subctxgm,gm} into
surface based analysis for left and right hemispheres. I want to inquire about
the sub cortical analysis.
1. I assume the analysis for sub cortical gray matter (i.e. using the images
subctxgm) is volumetric. Is this correct?
2. Are the following steps correct for sub cortical gray matter analysis
mri_vol2vol --mov subctxgm.nii.gz --reg reg.dat --tal --talres 2 --talxfm
talairach.xfm --nearest --no-save-reg --o subctxgm.tal2mm.nii.gz
mri_mask subctxgm.tal2mm.nii.gz
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
subctxgm.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
_______________________________________________
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.
