Which version of FS are you using? Can you send the
lh.Rossvolume.mgh.log file?
On 1/29/2021 3:54 PM, Mark Wagshul wrote:
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mris_preproc --qdec-long RossQdecFinal30May.txt --target fsaverage
--hemi lh --meas volume --out lh.Rossvolume.mgh
The vertex-wise analyses were run with 5 mm smoothing, but the graph I
showed below was created with the unsmoothed data.
Thanks for the help!
Mark
____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461
Ph: 718-430-4011
FAX: 718-430-3399
Email:_mark.wags...@einsteinmed.org <mailto:mark.wags...@einsteinmed.org>_
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*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve
*Sent:* Friday, January 29, 2021 11:41 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Voxel-wise volumes vs APARC volumes
What is your mris_preproc comman?
On 1/28/2021 5:34 PM, Mark Wagshul wrote:
* External Email - Use Caution *
Dear Freesurfer experts,
I’m stuck on something which I think has to do with how Freesurfer
calculates volumes, but can’t quite wrap my head around it,
hopefully you can enlighten me.
I have already produced robust results for our data using
region-based cortical volumes, using aparcstats2table. This is in
a group of 55 healthy older adults, modeling is using linear mixed
effects models. All volumes were normalized with the eTIV.
We were hoping on exploring the same models with voxel-wise
analyses, and are getting wildly different results. Data were
created using mri_preproc, resampled onto fsaverage, and my
assumptions was that because of this resampling, we should NOT be
normalizing these values to the eTIV. The same regions which were
highly significant on the region-based analyses and now not
significant at all, and other regions are now showing up as
significant.
Just as a sanity check, I attempted to reproduce the region-based
analyses with these data using the following simple (I thought!)
procedure:
1.Created an mgz mask of the region I’m interested in, using
mri_annotation2label and mri_label2label
2.Read my volume data (#subjects x #vertices) into Matlab
3.Read my mask into Matlab (yes, I know I can probably do this in
Freesurfer, but I’m more comfortable with Matlab!)
4.Multiply them together and take the sum across vertices.
5.Feed the resultant data back into my LME model.
Two things are puzzling to me. 1) The highly significant results
from the old LME are no longer significant (at the moment, only
checked for two of the cortical regions), and 2) The correlation
between these new data and the aparc volume are OK, although far
from perfect (R2 ~ 0.86).
So, I’m obviously missing something here. What is the difference
between the two volume calculation methods which could explain
these discrepancies?
Any help with this would be MOST appreciated!
Best,
Mark
____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461
Ph: 718-430-4011
FAX: 718-430-3399
Email:_mark.wags...@einsteinmed.org
<mailto:mark.wags...@einsteinmed.org>_
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