It is normal that those give different results. I would expect them to
be extremely close to each other, so small that the difference does not
matter. But if you had to take one, I'd take the output of
mris_anatomical_stats
On 4/5/2021 11:47 AM, Alberto Del Cerro Leon wrote:
External Email - Use Caution
To obtain de stats from mri_anatomical stats i used
/>>mris_anatomical_stats -a
/usr/local/freesurfer/subjects/218/label/rh.myAAL.annot
-f///usr/local/freesurfer/subjects/218/stats/rh.myAAL.stats -b 218 rh/
In another hand, the workflow to obatian the stats from mri_segstats was:
>>/mri_aparc2aseg --s 218 --labelwm --hypo-as-wm --rip-unknown --volmask
--o /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz //--annot myAAL/
/>>//mri_segstats --seg
/usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz//--ctab
/home/neuroimage/fsl/FreeSurfer/wmAALColorLUT.txt --sum
/usr/local/freesurfer/subjects/218/stats/wmmyAAL.stats /
/-//-pv /usr/local/freesurfer/subjects/218/mri/norm.mgz --excludeid 0
--brainmask /usr/local/freesurfer/subjects/218/mri/brainmask.mgz --in
/usr/local/freesurfer/subjects/218/mri/norm.mgz/
/--in-intensity-name norm --in-intensity-units MR --subject 218
--surf-wm-vol --etiv/
El lun, 5 abr 2021 a las 15:50, Douglas N. Greve
(<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>) escribió:
What are your command lines?
On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<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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