Hi Thomas, I have done the mri_surf2surf all all old data and everything went OK. Thanks for your help.
Now I need to extract the NEW cortical thickness based on this new parcellation. I am saying NEW because I extracted the cortical thickness last year without running the mri_surf2surf. We think the new cortical thickness will be different from the one we extracted last year due to the use of new ATLAS. Are we correct? Many thanks in advance, Ali On Sun, Sep 20, 2015 at 3:33 AM, Thomas Yeo < > > ytho...@csail.mit.edu> wrote: > >> Hi Ali, >> >> It should work with the old processed data. >> >> --Thomas >> >> On Sun, Sep 20, 2015 at 12:00 AM, Ali Radaideh <ali.radai...@hu.edu.jo> >> wrote: >> > Dear Thomas, >> > >> > Many thanks for your detailed explanation. I will try it and let you >> know. >> > >> > One more question please, last year, I processed another set of subjects >> > using an older version of FreeSurfer 5.0. Now the old version has been >> > replaced with its new one (5.3.0) on the same PC. In other words, my PC >> has >> > the new version of freesurfer 5.3.0 and two sets of processed T1 >> images. One >> > set was processed using the old version of freesurfer which is no longer >> > there. The other set was processed using the new version. So, can I >> > transform the network atlases to the set of subjects spaces processed >> last >> > year using the old version of freesurfe 5.0.0r? or or I have to re-run >> the >> > recon-all again? >> > >> > Many thanks in advance and my apology for keeping you busy with my >> > questions. >> > >> > Ali >> > >> > >> > On Sat, Sep 19, 2015 at 3:14 PM, Thomas Yeo <ytho...@csail.mit.edu> >> wrote: >> >> >> >> Hi Ali, >> >> >> >> Sorry, I wasn't clear. The 7 and 17 network atlases are released with >> >> FreeSurfer 5.3. In particular, the "annot" files are found in >> >> $FREESURFER_HOME/subjects/fsaverage/label/. Therefore since you have >> >> already run recon-all using FreeSurfer, then this means that you do >> >> not need to "save" the new atlas anywhere. >> >> >> >> The 7 and 17 network atlases are in fsaverage space. You can run the >> >> following commands to transform the atlases to your individual >> >> subjects' surfaces. Suppose your subject is called 100306_QD95CU_FS >> >> and the recon-all of this subject is located in >> >> /share/users/imganalysis/yeolab/data/GSP/. >> >> >> >> 1) The first step is to set the variable SUBJECTS_DIR to point to >> >> where your subject is: >> >> >> >> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/ >> >> >> >> 2) The second step is to create a symbolic link so that the FreeSurfer >> >> "fsaverage" subject appears to be in your SUBJECTS_DIR >> >> >> >> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage >> >> >> >> 3) The final step is to run mri_surf2surf to transform the 7 network >> >> atlas to your subject's native surfaces. >> >> >> >> >> mri_surf2surf --srcsubject fsaverage --trgsubject 100306_QD95CU_FS >> >> >> --hemi lh --sval-annot >> >> >> >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot >> >> >> --tval >> $SUBJECTS_DIR/100306_QD95CU_FS/label/lh.Yeo2011_7Networks_N1000.annot >> >> >> >> Note that the above is only for the left hemisphere. You can replace >> >> all the "lh" with "rh" to transform the right hemisphere instead. >> >> >> >> Note that the above is for the 7 networks. You can replace all the "7" >> >> with "17" to transform the 17-network atlas instead. >> >> >> >> I hope the above is clearer. Let me know if you have other questions. >> >> >> >> --Thomas >> >> >> >> On Sat, Sep 19, 2015 at 4:16 PM, Ali Radaideh <ali.radai...@hu.edu.jo> >> >> wrote: >> >> > Also, could you please direct me in which directory I should save the >> >> > new >> >> > atlas? >> >> > >> >> > Thanks, >> >> > Ali >> >> > >> >> > On Sat, Sep 19, 2015 at 9:47 AM, Thomas Yeo <ytho...@csail.mit.edu> >> >> > wrote: >> >> >> >> >> >> Hi Ali, >> >> >> >> >> >> May I confirm that your data is T1 and not functional data? Here's >> >> >> what you can do to transfer the parcellation to your individual >> >> >> subject's surface mesh. After that you can use the usual commands to >> >> >> extract thickness, etc. >> >> >> >> >> >> In your shell (assuming you are using c shell) >> >> >> >> >> >> # First set variable s to be subject id >> >> >> >> set s = 100306_QD95CU_FS >> >> >> >> >> >> # set freesurfer environmental variable SUBJECTS_DIR to point to >> where >> >> >> the data is >> >> >> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/ >> >> >> >> >> >> # use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR >> >> >> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ >> $SUBJECTS_DIR/fsaverage >> >> >> >> >> >> # use "-sval-annot" option to transfer annotation >> >> >> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh >> >> >> >> --sval-annot >> >> >> >> >> >> >> >> >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot >> >> >> >> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot >> >> >> >> >> >> # use "sval" option to transfer confidence map. >> >> >> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh >> >> >> >> --sval >> >> >> >> >> >> >> >> >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz >> >> >> >> --tval >> >> >> >> $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz >> >> >> >> >> >> Cheers, >> >> >> Thomas >> >> >> >> >> >> On Sat, Sep 19, 2015 at 3:12 PM, Ali Radaideh < >> ali.radai...@hu.edu.jo> >> >> >> wrote: >> >> >> > Dear FreeSurfer experts, >> >> >> > >> >> >> > I have finished processing a group of brains MR images collected >> at >> >> >> > 7T >> >> >> > scanner using freesurfer 5.3.0 (Ubuntu 64 bits machine). >> >> >> > >> >> >> > However, we need to get the cortical parcellation based on >> functional >> >> >> > network connectivity. So I have downloaded the Atlas data >> >> >> > (Yeo_JNeurophysiol11_FreeSurfer) to use it for the parcellation >> but I >> >> >> > have >> >> >> > few questions which I hope you will be able to help me on. >> >> >> > >> >> >> > 1- Do I need to repeat the "recon-all" process? >> >> >> > 2- If yes, how can I change the default Atlas that freesurfer >> uses? >> >> >> > 3- If no, what can I do to get the cortical parcellation based on >> >> >> > finctional >> >> >> > networks from our processed data? >> >> >> > 4- At the end, shall I use the usual commands to extract the >> volumes, >> >> >> > thicknesses ...etc? >> >> >> > >> >> >> > >> >> >> > Many thanks for your help in advance. >> >> >> > >> >> >> > Ali >> >> >> > >> >> >> > >> >> >> > -- >> >> >> > Ali M. Al-Radaideh. PhD >> >> >> > Head of Department of Medical Imaging >> >> >> > Vice Dean of the Faculty of Allied Health Sciences >> >> >> > The Hashemite University, >> >> >> > Zarqa, Jordan >> >> >> > W.phone +962 5 3903333 ext.5422, 5355, 5364 >> >> >> > Email: ali.radai...@hu.edu.jo >> >> >> > webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= >> >> >> > >> >> >> > >> >> >> > _______________________________________________ >> >> >> > 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. >> >> >> > >> >> >> _______________________________________________ >> >> >> Freesurfer mailing list >> >> >> Freesurfer@nmr.mgh.harvard.edu >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >> >> > >> >> > >> >> > >> >> > -- >> >> > Ali M. Al-Radaideh. PhD >> >> > Head of Department of Medical Imaging >> >> > Vice Dean of the Faculty of Allied Health Sciences >> >> > The Hashemite University, >> >> > Zarqa, Jordan >> >> > W.phone +962 5 3903333 ext.5422, 5355, 5364 >> >> > Email: ali.radai...@hu.edu.jo >> >> > webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= >> >> > >> >> > >> >> > _______________________________________________ >> >> > 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. >> >> > >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > >> > >> > -- >> > Ali M. Al-Radaideh. PhD >> > Head of Department of Medical Imaging >> > Vice Dean of the Faculty of Allied Health Sciences >> > The Hashemite University, >> > Zarqa, Jordan >> > W.phone +962 5 3903333 ext.5422, 5355, 5364 >> > Email: ali.radai...@hu.edu.jo >> > webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= >> > >> > >> > _______________________________________________ >> > 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. >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > > -- > > > > > > > > *Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of > the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, > JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: > ali.radai...@hu.edu.jo <ali.radai...@hu.edu.jo>* > *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= > <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>* > > -- *Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radai...@hu.edu.jo <ali.radai...@hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*
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