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?
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD5cHD7GRwSEtVGA5l0wVfI-qwadg-4V9ONf5EZ0kiLcRjW6DVI_Rd2ZeqiMxXTIBEnUxA3T9NzdNSt8iXVZ7cyXIzeEsQeBhrig9ume-iTSL61o9NJ8xeYD0zqzkN5beVGaw6yxXpHYMufcuWsp7li3hf1daYTVoJEiUno9_8hA_Q7xVe54KZ585zoXC2r43bYx3pxJ56xQU1iAEqLf5WArPGhqVAV_6TmQ9v8C2Xw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/1G_h97ZZmS1M3Mu1WvIxpTpCamKUMZrdeii7Mb-_WyhLnqexfnx4M_Pdm9J5uI07IHMoSLX06nTKmLoGpCM__s_0BMxj3yFWmG-DrcG6_hwmbQ4lmwutoIJ7LgzXFCY1kq67Vh2ew-rSx7g1EsGVdqylYYD-iDG_k-YXsbd2bEshDXD1Qem3t3Vtnd2vU-YadqAhVEksxzWDJrWr5lnPwyL89yQGUfLXDJIiRGxyCQZxSHNkSoSCXq9BCZ85lPb6M33BVmSYeBvf-nyCBHvN7NQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/1G_h97ZZmS1M3Mu1WvIxpTpCamKUMZrdeii7Mb-_WyhLnqexfnx4M_Pdm9J5uI07IHMoSLX06nTKmLoGpCM__s_0BMxj3yFWmG-DrcG6_hwmbQ4lmwutoIJ7LgzXFCY1kq67Vh2ew-rSx7g1EsGVdqylYYD-iDG_k-YXsbd2bEshDXD1Qem3t3Vtnd2vU-YadqAhVEksxzWDJrWr5lnPwyL89yQGUfLXDJIiRGxyCQZxSHNkSoSCXq9BCZ85lPb6M33BVmSYeBvf-nyCBHvN7NQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/1ekuMRUoFakA2GcA-HAYdzP-YJXE02k2qNXi0TJVuyogwG91AjL1ZBmUrTsH4uVppkOxMsSjpGieAeNogSOH-B4xx5g9unahzAc5C3ej66181XPQbOyF-QGM3IiysY85C2K3kUDwUnIZU0bpa6puHpvIZjLD3nhAp5OfMoayKhs_3KQu2Of-pNFnkKv4aCDH5bgpGDz9VcW-tGQIUIAt172I-tNHanxfB2OHj9nNbVaEInREVZwtxJM_jFMf0lLIXT5gJHIRKX0q_RgpAUoygww/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/1ekuMRUoFakA2GcA-HAYdzP-YJXE02k2qNXi0TJVuyogwG91AjL1ZBmUrTsH4uVppkOxMsSjpGieAeNogSOH-B4xx5g9unahzAc5C3ej66181XPQbOyF-QGM3IiysY85C2K3kUDwUnIZU0bpa6puHpvIZjLD3nhAp5OfMoayKhs_3KQu2Of-pNFnkKv4aCDH5bgpGDz9VcW-tGQIUIAt172I-tNHanxfB2OHj9nNbVaEInREVZwtxJM_jFMf0lLIXT5gJHIRKX0q_RgpAUoygww/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
