External Email - Use Caution
Hi Catherine,
We have extracted the 7 and 17 networks into 51 and 114 regions respectively. See figures in https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce...
Unfortunately, we have only provided the parcellation in fsaverage5 ( https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce...), so you should add one more mri_surf2surf step to upsample the parcellation from fsaverage5 to fsaverage. Check that it is good and then proceed with your previous steps.
I am emailing the freesurfer list, so that my reply might hopefully be useful for other folks.
Regards, Thomas
On Thu, May 3, 2018 at 8:46 AM, Catherine Joe catherine.joe@uq.net.au wrote:
Hello Dr Yeo,
Yes, I want to be able to split network 3 into different component regions so that I can have a nii file for FEF. This will then allow me to get the signal intensity and hopefully, the volume of the FEF region for each participant in my Honour's project.
Thank you.
Kind regards,
Catherine
*From:* Thomas Yeo ythomas@csail.mit.edu *Sent:* Thursday, 3 May 2018 9:36:52 AM
*To:* Catherine Joe *Cc:* 李婧玮 *Subject:* Re: Fw: Yeo Atlas Network 3 segmentation FEF
Hi Catherine,
Can I verify what you need is network 3 split into different component regions like FEF, etc?
Regards, Thomas
On Wed, May 2, 2018 at 11:08 AM Catherine Joe catherine.joe@uq.net.au wrote:
Hi Dr Yeo and Jingwei,
Yes, I did use that link to subscribe to the mailing list about 2.5 weeks ago and they still haven't gotten back to me. I simply thought I didn't get a confirmation email and tried again, which was the message I forwarded to you today. Just now, I tried subscribing again.
So the commands I've used so far is as follows:
mri_surf2surf --srcsubject fsaverage --trgsubject subject11GS --hemi lh --sval-annot $subjectdir/Yeo_Neurophysiol11_Freesurfer/ fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval lh.7Networks.annot
(same was done for the rh before doing mri_aparc2aseg)
mri_aparc2aseg --s subject11GS --o $subjectdir/subject11GS/test/test.mgz --annot 7Networks --annot-table path_to/Yeo2011_7Networks_colorlux.txt
mri_annotation2label --subject subject11GS --outdir $subjectdir/subject11GS/test --hemi lh --annotation $subjectdir/subject11GS/label/lh.7Networks.annot
mri_label2vol --label $subjectdir/subjet11GS/test/lh.7Networks_3.label --temp $subjectdir/subject11GS/mri/rawavg.mgz --subject subject11GS --hemi lh 00o $subjectdir/subject11GS/test/lh7Networks.nii.gz --proj frac 0 1 0.01 --reg $subjectdir/subject11GS/corticalroi/subject11GS_ register.dat
And after doing that, all I got was the volume for network 3 but not actually having any separation with the FEF and the other areas.
Thank you for your help.
Kind regards,
Catherine
*From:* yeoyeo02@gmail.com yeoyeo02@gmail.com on behalf of Thomas Yeo < ythomas@csail.mit.edu> *Sent:* Wednesday, 2 May 2018 10:33:18 AM *To:* Catherine Joe *Cc:* 李婧玮 *Subject:* Re: Fw: Yeo Atlas Network 3 segmentation FEF
Hi Catherine,
Have you tried subscribing to the mailing here ( http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)?
Can you please let me know the exact commands you have tried so far?
I am cc-ing my grad student (Jingwei), who might be able to answer more rapidly. Please reply all to keep her in the loop.
Thanks, Thomas
On Wed, May 2, 2018 at 8:14 AM, Catherine Joe catherine.joe@uq.net.au wrote:
Hi Dr Yeo,
Thank you for your help before with actually aligning and extracting your atlas. I know that you mentioned before that I should try and email into the FreeSurfer mailing list for any further queries.
However, as you can see, I am apparently not subscribed to the list even though I sent in a request before. I've been trying to send in a question for the past week.
I was wondering if you'd be able to help me with this problem I've had after extracting the Network 3 ROI. The message I tried sending to the FreeSurfer Mailing list is as below:
Hello,
I'm having trouble getting the segmentation for the FEF using the Yeo Atlas 2011 Network 3. Although I've been able to get Network 3 as a volume file, it doesn't show me two individual labels for the network (primarily the three areas of the dorsal attention network). In Freesurfer, it simply has all three areas labelled as the same colour called the 'left cerebral exterior'. I even did mri_aparc2aseg using the following code:
mri_aparc2aseg --s subject11GS --o /data/cai-wks2/data _local_temp/Cathy/freesurfersubjects/subject11GS/test/test.mgz --annot 7Networks --annot-table path_to/Yeo2011_7Networks_colorLUT.txt
I am still unable to find the labels that qualify as FEF for the lh or rh so that I could mask out the values in the mgz file and then extract the information I want from the roi (a stats on the grey matter volume as well as the signal intensity).
Any help would be greatly appreciated.
Kind regards,
Catherine
Thank you so much for your time.
Kind regards,
Catherine
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-owner@nmr.mgh.harvard.edu <freesurfer-owner@nmr.mgh.harvard.edu
*Sent:* Wednesday, 2 May 2018 10:10 AM *To:* Catherine Joe *Subject:* Yeo Atlas Network 3 segmentation FEF
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---------- Forwarded message ---------- From: Catherine Joe catherine.joe@uq.net.au To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Cc: Bcc: Date: Wed, 2 May 2018 00:10:33 +0000 Subject: Yeo Atlas Network 3 segmentation FEF
External Email - Use CautionHello,
I'm having trouble getting the segmentation for the FEF using the Yeo Atlas 2011 Network 3. Although I've been able to get Network 3 as a volume file, it doesn't show me two individual labels for the network (primarily the three areas of the dorsal attention network). In Freesurfer, it simply has all three areas labelled as the same colour called the 'left cerebral exterior'. I even did mri_aparc2aseg using the following code:
mri_aparc2aseg --s subject11GS --o /data/cai-wks2/data _local_temp/Cathy/freesurfersubjects/subject11GS/test/test.mgz --annot 7Networks --annot-table path_to/Yeo2011_7Networks_colorLUT.txt
I am still unable to find the labels that qualify as FEF for the lh or rh so that I could mask out the values in the mgz file and then extract the information I want from the roi (a stats on the grey matter volume as well as the signal intensity).
Any help would be greatly appreciated.
Kind regards,
Catherine
freesurfer@nmr.mgh.harvard.edu
-
Thomas Yeo