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
