Hi Kari
what do you mean when you say "when I look at them in freeviewer the voxels are definitely not in the correct spot". Do you mean the spectroscopy voxels?
cheers Bruce
On Fri, 22 Jul 2016, Kari Parsons wrote:
Hi Bruce,
Yes, I agree it doesn't seem right. They're LAG and ACG (I'm usingspectroscopy voxels as my ROIs). The surfaces look reasonable when I'm running through the suggested steps on the freesurfer website for getting the surface thickness when using an roi as a mask, but when I look at them in freeviewer the voxels are definitely not in the correct spot (they're pretty far off).
The acquisition parameters for the scan were pretty standard (BRAVOsequence with 1 mm^3 isotropic voxels). The steps that I ran through with the spectroscopy voxel were:
tkmedit -f ${subj_T1} -overlay ${spectroscopy_voxel_mask} -fthresh 0.5
mri_vol2surf --mov ${spectroscopy_voxel_mask} --hemi lh --out lh.${subj_number}.ACG.mgh
cd ${subj_number}/surf
tksurfer ${subj_number} lh inflated -overlay lh.${subj_number}.ACG.mgh -fthresh 0.5
mri_surf2surf --s ${subj_number} --trgsubject ${subj_number} --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh --reshape
mri_segstats --seg lh.${subj_number}.ACG.mgh --in ${subj_number}/surf/lh.thickness.fsaverage.mgh --sum segstats-${subj_number}.txt
Thanks very much, Kari
On 2016-06-02, at 6:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Kari
the average thickness in some ROIs is 5mm??? Like which ones? That certainly seems like something is wrong. Do the surfaces look accurate? What were the parameters/resolution/sequence of the data you gave to recon-all?
cheers Bruce
On Fri, 3 Jun 2016, Kari Parsons wrote:
Hi,
I'm using ROI masks (spectroscopy voxels) to get cortical thickness values. I'm pretty much following the tutorial online ('VolumeRoiCorticalThickness') as I'm quite new to Freesurfer. It looks like Freesurfer has a maximum of cortical thickness ceiling at 5 mm, and I'm getting that as the maximum cortical thickness for a fair number of subject's ROI. I'd really like to hear thoughts on this: if it might be indicative of some error happening and if my mean or range cortical thickness is going to be thrown off by it?
Thanks for your help, Kari
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