Hi Bruce,
Yes, I agree it doesn't seem right. They're LAG and ACG (I'm using
spectroscopy 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 (BRAVO
sequence 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 <fis...@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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>>
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