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_parcellation/Yeo2011_fcMRI_clustering Unfortunately, we have only provided the parcellation in fsaverage5 ( https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels), 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....@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 <ytho...@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....@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:* yeoye...@gmail.com <yeoye...@gmail.com> on behalf of Thomas Yeo < > ytho...@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....@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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of > freesurfer-ow...@nmr.mgh.harvard.edu <freesurfer-ow...@nmr.mgh.harvard.edu > > > *Sent:* Wednesday, 2 May 2018 10:10 AM > *To:* Catherine Joe > *Subject:* Yeo Atlas Network 3 segmentation FEF > > You are not allowed to post to this mailing list, and your message has > been automatically rejected. > > ! IMPORTANT ! Make sure you are sending your message using the same > email address that was used to subscribe to the list! > > !! Registering for a FreeSurfer license does not mean you have been > subscribed to the list !! > > If you think that your messages are being rejected in error, contact > the mailing list owner at freesurfer-ow...@nmr.mgh.harvard.edu > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > ---------- Forwarded message ---------- > From: Catherine Joe <catherine....@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 Caution > > 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 > > > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
