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I got the idea but faced an issue with mris_preproc, the command is:
mris_preproc --target 0_1 --s avg_subject_91_noexpopts --hemi lh --meas
thickness --out avg_91_to_lh.mgh
where 0_1 is target patient to map thickness, from avg_subject_91_noexpopts,
optained from make_average_subject.
i get the error running mris_preproc:
Reading source surface reg
/input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg
No such file or directory
mri_surf2surf: could not read surface
/input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg
No such file or directory
Why there should be lh.0_1.sphere.reg? Have i missed some intermediate steps??
________________________________
От: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> от имени Douglas N. Greve
<dgr...@mgh.harvard.edu>
Отправлено: 3 февраля 2020 г. 20:51
Кому: freesurfer@nmr.mgh.harvard.edu
Тема: Re: [Freesurfer] Thickness group normalization
Do you have a group of subjects that you want to use as an average? If so, you
can just map all their thickness maps to your patient subject with
mris_preproc --target patientsubjectname [then usual arguments]
Compute the mean with
mri_concat outputofmris_preproc.mgz --mean --o groupmean.mgz
You can then compare groupmean.mgz to your patient on a vertex-by-vertex baiss
On 2/3/2020 12:16 PM, Vyacheslav Yarkin wrote:
External Email - Use Caution
Hello Freesurfer Team,
Would you be so kind to provide freesurfer steps to implement warping fsaverage
mean thickness data on individual subject inflated brains ?
I am using expert opts to disable cortical thickness restriction, and set
mris_thickness -max 20 as I want to find fcd to cortical surfaces. The reason i
need normalization is that there is zones like sulci orbitales have bigger
thickness accross subjects group ( control ) and have red LUTs on inflated
thickness map. So i would like to normalize thickness over control group, to
use it on patients to exclude "normal" thickness excedings to include only
increased FCD zones. The main issue I faced is how to warp fsaverage mean
thickness data on individual subject's inflated brain as they have vertices
number missmatch.
Steps I tried:
1) make_average_subject
2) mri_concat --mean to create mean thicknesses over group?
Thank you
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