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

[Aihuiping Xue]

External Email - Use Caution

Dear Freesurfer users,

We have fixed the issue.

In our previous Yeo2011 split components parcellation (version b in Ruby’s
email), the colortable inside these annot files contain ROIs from both
hemisphere. This will cause some problems when you want to project the
parcellation to individual volume space with mri_aparc2aseg.
To resolve this issue, we have updated these annot files, where the
colortable are now separated. Please visit this link to download our
updated annot files:

https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label

We also provide a tutorial of projecting Yeo2011 parcellation to individual
subjects, which include the procedure of: 1) project to individual surface,
2) project to individual volume, and 3) visualize the parcellations in
individual space.

Please visit this link for details:

https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/project_to_individual

Best Regards,
XUE Aihuiping

On Thu, Mar 28, 2019 at 11:05 AM Ruby Kong  wrote:

> 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 
> 

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

[stdp82]

External Email - Use CautionHi,please, could you suggest colortable for 7 network?Thanks!StefanoIl 27 marzo 2019 alle 16.10 Thomas Yeo  ha scritto:  External Email - Use Caution Hi Stefano,Did you see the colortable that Aihuiping attached? Does it work for you?Thanks,ThomasOn 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,ThomasOn 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.ThanksStefanoIl 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,ThomasOn 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.txtWhen 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?ThanksBest regards,StefanoIl 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, ThomasOn 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,ThomasOn 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_N1000mri_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.annottkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgzThe 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?ThanksStefanoIl 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 CautionI 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 

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

[stdp82]

External Email - Use CautionThanks!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_N1000mri_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_N1000mri_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.txtIl 28 marzo 2019 alle 4.05 Ruby Kong  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 versionMay 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.annotIn 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.annotAs 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 tablesMy 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 hemisphereAccording 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 

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

[Ruby Kong]

External Email - Use Caution

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  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  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  ha
>> scritto:
>>
>> External Email - Use Caution
>>
>>
>> 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 

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

[Thomas Yeo]

External Email - Use Caution

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  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  ha
> scritto:
>
> External Email - Use Caution
>
>
> 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:
>
> 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 (
> 

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

[stdp82]

External Email - Use Caution

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  ha scritto:
> 
> 
> External Email - Use Caution
> 
>  
> 
> 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 
> mailto: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 mailto: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 mailto: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 mailto: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 mailto: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.
> > > > > > 
> > > > > >   

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

[stdp82]

External Email - Use Caution

Additional issue: the colortable does not fit with the atlas and with anatomy 
of networks.

> Il 27 marzo 2019 alle 16.17 Thomas Yeo  ha scritto:
> 
> 
> External Email - Use Caution
> 
>  
> 
> 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 
> mailto: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 mailto: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 mailto: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 mailto: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 mailto: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 
> > > > > > 

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

[stdp82]

External Email - Use Caution

Thanks the right hemiphere is ok, but the left no.

> Il 27 marzo 2019 alle 16.17 Thomas Yeo  ha scritto:
> 
> 
> External Email - Use Caution
> 
>  
> 
> 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 
> mailto: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 mailto: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 mailto: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 mailto: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 mailto: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 
> > 

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

[Thomas Yeo]

External Email - Use Caution

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  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  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:
>
> 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 

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

[stdp82]

External Email - Use Caution

The problem persists.

We are sure that the command lines which I'm using are corrected?

> Il 27 marzo 2019 alle 16.10 Thomas Yeo  ha scritto:
> 
> 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 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > Please see the attached file.
> > 
> > 
> > > > > Il 27 marzo 2019 alle 15.39 Thomas Yeo < 
> > ytho...@csail.mit.edu mailto: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 
> > > mailto: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 mailto: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 mailto: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 
> > > > > > mailto: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 mailto: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 
> > > > > > > > mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > > > > > 
> > > > > > > > > Hi Stefano,
> > > > > > > > > 
> 

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

[stdp82]

External Email - Use Caution

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  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 mailto: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 mailto: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 
> > > mailto: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 mailto: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 mailto: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 
> > > > > > mailto: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 

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

[Thomas Yeo]

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  wrote:

> Please see the attached file.
>
>
> Il 27 marzo 2019 alle 15.39 Thomas Yeo  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 

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

[stdp82]

External Email - Use Caution

Please see the attached file.


> Il 27 marzo 2019 alle 15.39 Thomas Yeo  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 
> mailto: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 mailto: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 
> > > mailto: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 mailto: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 mailto: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 
> > > > > > mailto: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
> > > > > > > 
> > > > > > > 

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

[Thomas Yeo]

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  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  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
> 

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

[stdp82]

External Email - Use Caution

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  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 
> mailto: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 mailto: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 
> > > mailto: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 mailto: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 mailto: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 
> > > > > > 

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

[Thomas Yeo]

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  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  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 
>  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 

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

[stdp82]

External Email - Use Caution

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  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 
> mailto: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 mailto: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 
> > > mailto: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 
> > > > mailto: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 
> > > > > mailto:std...@virgilio.it wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > External Email - Use Caution
> > > > > > 
> > > > > > I will use freeview.
> > > > > > 
> > > > > > Have you any suggestion on the use of 
> > > > > > fcseed-config option?
> > > > > > 
> > > 

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

[Thomas Yeo]

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  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  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 
>  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 
>  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
>
> 

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

[stdp82]

External Email - Use Caution

mri_aparc2aseg --s subj --o sub/mri/Yeo_17Net.mgz --annot 
Yeo2011_17Networks_N1000 --annot-table 
/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt
freeview subj orig.mgz -ov subj/mri/Yeo_17Net.mgz

I am not sure that the command line sound fine.

When I open the files in freeview, the name of labels is the same of aparc2009.

> Il 26 marzo 2019 alle 4.01 Thomas Yeo  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 
> mailto: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 mailto: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 
> > > mailto: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 
> > > > >  mailto: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
> > > > > 

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

[stdp82]

External Email - Use Caution

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  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 
> mailto: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 mailto: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 
> > > mailto: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 
> > > > >  mailto: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 
> > > > > mailto:std...@virgilio.it wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > External Email - Use Caution
> > > > > > 
> > > > > > Thanks.
> > > > > > 
> > > > > >   

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

[Thomas Yeo]

External Email - Use Caution

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  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 
>  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 
>  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."
>   ha scritto:
>
> You have to convert 

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

[stdp82]

External Email - Use Caution

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." 
>  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 mailto: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 
> > >  mailto: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 
> > > mailto: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 
> > > >  mailto: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 
> > > > mailto: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
> > > >  

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

[Greve, Douglas N.,Ph.D.]

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 
 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 
 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."
 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

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

[stdp82]

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

[Greve, Douglas N.,Ph.D.]

Load it as a segmentation, not an overlay (-seg Yeo_17Net.mgz)

On 3/10/19 4:46 AM, 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 
 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.Yeo2011_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_ColorLUT_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." 
mailto: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_clustering).

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

[Bruce Fischl]

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  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."
 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

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

[stdp82]

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  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 
> mailto: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.Yeo2011_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_ColorLUT_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." 
> > > mailto: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 
> > > mailto: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_clustering).
> > > > 
> > > > 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 
> > > > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > > 
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > 
> > > > > > > 
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu 
> > > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > 
> > > > > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > > ___
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

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  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.Yeo2011_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_ColorLUT_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_clustering
> ).
>
> 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
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>
> ___
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>
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

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.Yeo2011_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_ColorLUT_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." 
>  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_clustering).
> > 
> > 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
> > 
> > > 
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Hi Stefano,

You can try the following

1) *Transform from fsaverage to subject's surface*
mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot
(repeat for rh)

2) *Transform from subject's surface into your subject's volume*
mri_aparc2aseg --s yoursubject --annot Yeo_17Network_native --o
$SUBJECTS_DIR/yoursubject/mri/outputfile.mgz

One thing to note: "mri_aparc2aseg" will automatically add 1000 for left
cerebral cortex voxels and add 2000 for right cerebral cortex voxels.
Therefore, for example, a left hemisphere voxel in network 5 will have a
value of 1005 in your outputfile.mgz.

Thanks,
Thomas

On Fri, Mar 8, 2019 at 7:29 PM  wrote:

> External Email - Use Caution
>
> Hi Doug,
>
> my apologies, I have tried to do it with some errors. Could you suggest
> the command line, please?
>
> 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_clustering
> ).
>
> 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

[stdp82]

External Email - Use Caution

Hi Doug,

my apologies, I have tried to do it with some errors. Could you suggest the 
command line, please?

Stefano

> 
> Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." 
>  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_clustering).
> > 
> > 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
> > 
> > > 
> ___
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

Hi Bruce,

my apologies, I have tried to do it with some errors. Could you suggest the 
command line, please?

Stefano

> 
> Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." 
>  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_clustering).
> > 
> > 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
> 
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[Greve, Douglas N.,Ph.D.]

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_clustering).
>  
>
> 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


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[Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

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_clustering).
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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