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:
- 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.htmlthat for static PET images, #3~5 will be different. Could you explain how I would need to enter the command differently?
- 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
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