1 Oct
2015
1 Oct
'15
3:43 p.m.
sure, you can use mri_segstats to get stats from it Bruce On Thu, 1 Oct 2015, Ali Radaideh wrote:
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 fischl@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 <greve@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 <greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@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.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> > <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@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 > greve@nmr.mgh.harvard.edu <mailto:greve@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.radaideh@hu.edu.jo <mailto:ali.radaideh@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 greve@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.radaideh@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.radaideh@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. 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.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=