Can we get any stats from this type of parcellation? I only can see two annotation files after running the mri_surf2surf command and these can be loaded tksurfer as an overlay.
Thanks, Ali On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > that will generate a parcellation on the individual subject surface of > Thomas Yeo's 17-network clustering. It won't do anything with the thickness > though. What are you trying to do? > > On Tue, 29 Sep 2015, Ali Radaideh wrote: > > mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh >> >> --sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot >> --tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot >> >> scz10 is my subject name >> >> On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu >> > >> wrote: >> what is your surf2surf command? >> >> On 9/28/15 5:11 PM, Ali Radaideh wrote: >> Dear Douglas, >> >> Thanks for your email. I meant to say that after running the >> recon-all, i ran the sur2surf command to get the cortical >> parcellation using Thomas Yeo Atlas. >> >> I thought that the extracted cortical thickness after running >> the surf2surf command will be different from the one extracted >> before running the command. But, Bruce kindly replied to my >> email saying that it is the same if it is calculated on >> vertex-wise basis. >> >> Thanks, >> Ali >> >> On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu> wrote: >> I can't understand what you are asking. Can you >> elaborate? >> >> On 09/28/2015 01:51 PM, Ali Radaideh wrote: >> > Thanks alot Douglas, >> > >> > Yes it is there but after checking it many time I >> found it corrupted >> > for some subjects due to copying them many times >> between machines. >> > >> > But May I ask you some thing related. I have just >> posted a question >> > regarding getting the cortical thickness after >> running the surf2surf >> > command (17 networks cortical parcellation). Now I >> found the stats >> > file not updated after running this command only >> the annotation files >> > in label folder. >> [rh.Yeo2011_17Networks_N1000.annot]. We thought that >> > using Yeo Atlas will give slightly different >> cortical thickness, are >> > we correct? >> > >> > Thanks, >> > Ali >> > >> > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve >> > <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > does that file exist? >> > >> > On 09/28/2015 01:05 PM, Ali Radaideh wrote: >> > > Dear FreeSurfer experts, >> > > After finishing the recon-all, I am trying >> to extract the cortical >> > > thickness for each subject and group them >> into one table but >> > > unfortunately i keep getting the following >> error: >> > > >> > > rh.aparc.DKTatlas40.stats is not found or is >> too small to be a >> > valid >> > > statsfile >> > > Use --skip flag to automatically skip bad >> stats files >> > > >> > > i tried to change the stats file (e.g I used >> aparc.a2009s) but I got >> > > the same error. >> > > >> > > I tried each brain alone and also got the >> same error. >> > > >> > > Any ideas please >> > > Thanks, >> > > 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 >> <mailto:ali.radai...@hu.edu.jo> >> > <mailto:ali.radai...@hu.edu.jo >> <mailto:ali.radai...@hu.edu.jo>> >> > > / >> > > /webpage: >> http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ >> > > >> > > >> > > >> > > >> _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 >> > Fax: 617-726-7422 >> > >> > Bugs: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: >> https://gate.nmr.mgh.harvard.edu/filedrop2 >> > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > Outgoing: >> > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > >> > >> _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto: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. >> > >> > >> > >> > >> > -- >> > /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 >> <mailto: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 >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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 >> >> >> >> _______________________________________________ >> 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. >> >> >> >> >> -- >> 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. > > -- *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=>*
_______________________________________________ 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.
