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

stdp82 Thu, 28 Mar 2019 12:09:37 -0700

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Thanks!
By these command lines the analysis are going fine.

mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.split_components.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.split_components.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/MNI152/Yeo2011_17network_SplitLabels_LUT_rh2058.txt

Il 28 marzo 2019 alle 4.05 Ruby Kong <roo.c...@gmail.com> ha scritto:
Hi Stefano,
We just figured out the issue. But there are a few things I might need to clarify with you:
1) Yeo2011 original parcellation or Yeo2011 split labels version
May I know which parcellation version you would like to use?
We provide two different versions of Yeo2011 parcellation annot files:
Version a. original parcellation: 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
In this version, each hemisphere contains 17 networks, for each hemisphere, the network labels start from 1 to 17 and medial wall area is indicated by 0.
Version b. split labels version: 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.split_components.annot
As each network might contain multiple distributed components, therefore, we split all networks into multiple components, and re-label these components.
In this version, each hemisphere contains 57 components, for left hemisphere, the component labels start from 1 to 57, for right hemisphere, the component labels start from 58 to 114.
In one of your earliest email (Mar 9th), you were running this command:
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
The above command will project the Yeo2011 original parcellation (version a) to individual surface space.
And then you run this one to project the parcellation from individual surface space to individual volumetric space:
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_ColorLUT_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
there is a very weird flag -sval-annot, which is not a valid flag in mri_aparc2aseg. For this flag you are using Yeo2011 spilt labels version (version b). But for the correct flag -annot, you pass in the output from mri_surf2surf, which uses the Yeo2011 original parcellation (version a).
2) freeview look up tables
My colleague Aihuiping thought you are using the Yeo2011 split labels version (version b), therefore she passed you the look up table txt files which you can use to visualize version b (i.e. Yeo2011_17network_SplitLabels_LUT_rh2058.txt).
But according to the commands in your last email, I assume you are actually using Yeo2011 original parcellation (version a). Therefore, the look up table txt file Yeo2011_17network_SplitLabels_LUT_rh2058.txt is not correct. That’s why you see the colors are wrongly mapped in freeview. If you would like to use version a, we can send you the look up table files for version a.
3) Different input subjects for left and right hemisphere
According to the commands in your last email, you are using subject subj as input for right hemisphere but subject ADNI001_AD for left hemisphere. It’s okay if you just want to do some quick test with different subjects, just want to confirm that you notice it. :)
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 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 subj/label/lh.Yeo2011_17Networks_N1000
Best,
Ruby

On Thu, 28 Mar 2019 at 07:54, Thomas Yeo < ytho...@csail.mit.edu> wrote:
Can you send us snapshots of what you are seeing? I am not sure what you mean by "labels of different colors that disagree with anatomical location and boundaries of the networks".

On Thu, Mar 28, 2019 at 12:08 AM < std...@virgilio.it> wrote:
My apologies, the right hemisphere does not contain the color of each region but only an unique color. The left hemisphere contains labels of different colors that disagree with anatomical location and boundaries of the networks.
If I use the original ColorLUT cointained in freeview (at opening) the anatomy of the networks of the file that is computed by mri_aprac2seg is ok but the labels is wrong.
Il 27 marzo 2019 alle 16.17 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:

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Hi Stefano,

How are you using the colortable? Are you just passing it as a flag to mri_aparc2aseg?

As far as I know (and I am NOT very knowledgeable, so I could be wrong), the volumetric file (Yeo_17Net.mgz) does not contain the color information. So when I said you should use the colortable, I meant you should use it with the viewer. I am not sure about tkmedit, but for freeview, you can load your volume and then also load your own colortable.

Regards,
Thomas

On Wed, Mar 27, 2019 at 11:13 PM < std...@virgilio.it> wrote:
The problem persists.
We are sure that the command lines which I'm using are corrected?
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 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 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/MNI152/Yeo2011_17network_SplitLabels_LUT_rh2058.txt

Il 27 marzo 2019 alle 15.40 Aihuiping Xue < xueaihuip...@gmail.com> ha scritto:

Hi Stefano,

I created a lookup table for your case. You can load your .mgz file and try this lookup table in freeview.

This is a temporary solution. We will modify the annot files and provide another version of lookup table. But that will take some time. I hope this lookup table can solve your problem for now.

Best Regards,
XUE Aihuiping

< std...@virgilio.it> 于2019年3月27日周三下午10:26写道：
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:

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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:

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

1) Yeo2011 original parcellation or Yeo2011 split labels version

2) freeview look up tables

3) Different input subjects for left and right hemisphere

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