Re: [Freesurfer] regions of Yeo 17 networks in fast

External Email - Use Caution

I will use freeview.

Have you any suggestion on the use of fcseed-config option?

Are you agree with the command line listed below?

fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite

My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?

How can I select a specific seed (id) to be used in -segids?

Thanks

Stefano

Il 10 marzo 2019 alle 17.17 Bruce Fischl <fischl@nmr.mgh.harvard.edu> ha scritto:

Hi Stefano

is there a reason you are using tkmedit and not freeview? We deprecated
tkmedit a long time ago now

cheers
Bruce
On Sun, 10 Mar 2019, stdp82@virgilio.it wrote:

    > > 

...

    External Email - Use Caution

    Thanks.

    My error is in tkmedit

    tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz

    Il 9 marzo 2019 alle 11.09 Thomas Yeo <ythomas@csail.mit.edu> ha scritto:

    External Email - Use Caution

    Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty?
    Your tkmedit command seems to assume Yeo_17Net.mgz is in
    /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder?

    On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it> wrote:

    External Email - Use Caution

    I have run:

    mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20
    11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000

    to check the output

    tksurfer subj rh inflated -annot
    $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot

    My concern is here:

    mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000
    --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU
    T_freeview.txt --sval-annot
    yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot

    tkmeditfv fsaverage orig.mgz -ov
    /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz

    Yeo_17Net.mgz is empty.

    Stefano

    Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D."
    <DGREVE@mgh.harvard.edu> ha scritto:

    You have to convert the annotation to a volume using mri_aparc2aseg
    (look at recon-all.log for an example, but note that you'll need to
    specify the output so that it does not overwrite). You'll then need to
    look in the output segmentation and see what the segmentation ids are

    On 3/7/19 4:13 PM, stdp82@virgilio.it wrote:
    >

    External Email - Use Caution

    Hi list,

    I'd like to use the regions included in Yeo 17 networks
    (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_cluste
    ring).

    in FS-FAST.

    Which is the command line to be used to create a segmentation in
    $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd
    like
    to use it to run fcseed-config, specify -seg yourseg.mgz
    -segid).

    Thanks

    Stefano

    _______________________________________________
    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 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 mailing list
    Freesurfer@nmr.mgh.harvard.edu
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

>