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
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:
make_average_subject
mri_concat --mean to create mean thicknesses over group
Thank you
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu от имени Douglas N. Greve dgreve@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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu от имени Vyacheslav Yarkin V.Yarkin@skoltech.ru Отправлено: 5 февраля 2020 г. 11:47 Кому: Freesurfer support list Тема: Re: [Freesurfer] Thickness group normalization
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu от имени Douglas N. Greve dgreve@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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You need to register your subjects to the new average subject with surfreg --s subject --t 0_1
On 2/11/2020 12:36 PM, Vyacheslav Yarkin wrote:
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu от имени Vyacheslav Yarkin V.Yarkin@skoltech.ru *Отправлено:* 5 февраля 2020 г. 11:47 *Кому:* Freesurfer support list *Тема:* Re: [Freesurfer] Thickness group normalization
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu от имени Douglas N. Greve dgreve@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:
make_average_subject
mri_concat --mean to create mean thicknesses over group
Thank you
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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Vyacheslav Yarkin