Hi Subin, I just created this page this morning http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer do you want to take a look and see if it answers your questions. As for #2, yes you still need to run gtmseg.
On 06/26/2016 07:45 AM, Lee Subin Kristine wrote: > > Hello, > > I am trying to use PVE correction on preprocessed PET data downloaded > from the Alzheimer's Disease Neuroimaging Initiative(ADNI) database. > I have a couple of questions: > > > 1) I am using the co-registered, averaged image of the dynamic images, > and it seems from your answers here > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html) > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html>that > > for static PET images, #3~5 will be different. Could you explain how I > would need to enter the command differently? > > 2) I already have segmentations of my MRI images obtained via > FreeSurfer(v.5.2)'s cortical parcellation. Would I still have to do > procedure #1 (gtmeseg --s subject) ? I did try using xcerebralseg > because it seemed from the help command that in my case where I > already have some FS segmentations that I should use this one: > > /You can use your own segmentation or a modified FS segmentation. // > //It will be easiest if you modify apas+head.mgz to insert your// > //segmentations. apas+head.mgz is created by gtmseg but you can// > //create it with // > / > /xcerebralseg --s $subject --o $SUBJECTS_DIR/$subject/mri/apas+head.mgz/ > > However when I do try I got the following error: > > /ERROR: could not open > /usr/local/freesurfer/subjects/002_S_4213/stats/002_S_4213/mri/apas+head.stats > > for writing// > //Errno: No such file or directory/ > > > > Thanks a lot in advance, > > Regards, > Subin > > > > _______________________________________________ > 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 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.
