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>) 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>) > 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>) 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>) 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>) >>>> 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 < >>>>> 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> >>>>> *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. 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