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

stdp82 Wed, 10 Apr 2019 09:04:08 -0700

External Email - Use Caution

Hi,

please, could you suggest colortable for 7 network?

Thanks!

Stefano

Il 27 marzo 2019 alle 16.10 Thomas Yeo <ytho...@csail.mit.edu> ha scritto:

        External Email - Use Caution

Hi Stefano,

Did you see the colortable that Aihuiping attached? Does it work for you?

Thanks,
Thomas

On Wed, Mar 27, 2019 at 11:08 PM < std...@virgilio.it> wrote:
Please see the attached file.

Il 27 marzo 2019 alle 15.39 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:

        External Email - Use Caution

Hi Stefano,

Can you attach your updated colortable, so we can take a look?

Thanks,
Thomas

On Wed, Mar 27, 2019 at 10:27 PM < std...@virgilio.it> wrote:
Yes the left hemisphere is fine.
The error occurs again. The labels for posterior DMN and anterior DMN are the same and numbered like 1016 and 2016, despite I have modified the txt.
Thanks
Stefano
Il 27 marzo 2019 alle 13.09 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:

        External Email - Use Caution

Hi Stefano,

Sorry. Can you confirm left hemisphere is ok?

I think in this version of the annot file, the right hemisphere regions will start off as 2058, rather than 2001. So instead of numbering from 2001 to 2057, it should be from 2058 to 2114.

Sorry about that. There are some intricacies between the annot format and mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, but not so soon.

Regards,
Thomas

On Wed, Mar 27, 2019 at 6:14 PM < std...@virgilio.it> wrote:
I have renumbered and run:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt
When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is visualized but labeled as rh_parahippocampal.
What's happened?
Thanks
Best regards,
Stefano
Il 26 marzo 2019 alle 13.05 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:

        External Email - Use Caution

Renumber for visualization purpose.

Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit.

Thanks,
Thomas

On Tue, Mar 26, 2019 at 6:44 PM < std...@virgilio.it> wrote:
Thanks.
Should I renumber for visualization purpose or for fs-fast?
How can I do it?

Il 26 marzo 2019 alle 4.01 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:

Hi Stefano,

Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?

If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while.

If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057.

Regards,
Thomas

On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it> wrote:
Hi, my concern is the mri_aparc2aseg command line.
In summary, I have done:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000

mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
The output is correct by the color label is those of aparc.
Probably the error is the match between the annotations and annot-table.
Could you check the command lines, please?
Thanks
Stefano

Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < dgr...@mgh.harvard.edu> ha scritto:

Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok.

On 3/10/19 4:05 PM, std...@virgilio.it wrote:
        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 <fis...@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, std...@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 <ytho...@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 < std...@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."
<dgr...@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, std...@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

_______________________________________________
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

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

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

Reply via email to