What are your command lines?
On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote:
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Thanks a lot, It works!, now I have obtained values to ctx and wm
volumes for each area. However when I look at the gray matter volume
values calculated by mri_anatomical stats, the results are pretty
similar to the ctx-ROIs calculated by mri_segstats, but not the same.
It is normal? In that case what measure will be more suitable?
El lun, 29 mar 2021 a las 5:22, Douglas N. Greve
(<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>) escribió:
You'll need to create your own color table by adding 3000 to the
left hemi structures and 4000 to the right hemi structures. Look
at the 3000s and 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt
On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote:
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Hello Douglas, i tried but when i look at the wmparc.mgz created
by the code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm
--rip-unknown --volmask --o mri/wmparc.mgz --annot myAAL it takes
the index and the names from FreeSurferColorLUT instead of the
names in the colorLUT associated with myAAL.annot then the ROIs
are disorganized. Could you help me with this problem?
El jue, 25 mar 2021 a las 14:59, Douglas N. Greve
(<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>) escribió:
Look in recon-all.log to find the command that creates the
wmparc.mgz. Run that command changing the aparc annot to your
annot and the output to a new file name. Look in
wmparc.stats; at the top will be an mri_segstats command
line. Copy that command line changing the file names as needed.
On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
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Thanks!, how can I obtain the white matter volume stats
using my annotation file?
El mar, 16 mar 2021 a las 16:59, Douglas N. Greve
(<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>)
escribió:
I think they will give very similar results, but my
guess is that #1 is a little better
On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
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I want to use the annotation file created by myself in
fsaverage to calculate the anatomical stats, but i
dont know what is the best workflow.
1. Convert the annotation file to each subject space
using mri_sur2surf and using mri_anatomical_stats in
each subject
2. Convert the surface of each subject to fsaverage
space and use mri_segstats to obtain the data, in this
case i dont know what surface i have to convert to
fsaverage space to do it (i can see thickness
(lh/rh.thickness) and volume (lh/rh.volume) but not
folding index and white matter volume)
Any idea?
El lun, 8 mar 2021 a las 16:04, Fischl, Bruce
(<bfis...@mgh.harvard.edu
<mailto:bfis...@mgh.harvard.edu>>) escribió:
Hi Alberto
1. And 4. Are not properties of single surfaces –
they are computed from the white and the pial.
For 2 and 3 that is really up to you
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
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<freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
*On Behalf Of *Alberto Del Cerro Leon
*Sent:* Monday, March 8, 2021 7:02 AM
*To:* Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* [Freesurfer] Problem with freesurfer
measures
* External Email - Use Caution *
Hello Freesurfer team, I am using an annotation
file that i've created previously to obtain the
measures of some ROIs. To do that i am using de
commands mri_surf2surf and mri_segstats. I want to
obtain the following measures:
1. Gray and White Matter Volume
2. Folding Index
3. Curvature measures
4. Thickness
However I don't know what surface in the surf
folder of each subject I have to use. Could u help me?
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