Hi Doug,
Thanks a lot for the page! It was very helpful.
I have a few questions about one of the commands and a question for one of the output files.
1) mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output
(a) For the psf flag, do I have to know exactly the FWHM of the point-spread function of the scanner or would a default value of 6 work for all? I am using PET images from multiple centers and thus each image are from different scanners, and I'm not sure how I would find the fwhm for each scanner.
(b) For the mgx flag, is the GM threshold .01 an optimal threshold referring to the p-value?(am new to PVEcorrection and asking out of curiosity) What is the difference if I enter .01 versus I don't enter it?
2) From the gtm.stats.dat output file, the 5th column(number of PET voxels in the ROI) of, for example, the ctx-lh-precuneus and ctx-rh-precuneus are 1744 and 1805 respectively. However, in the ?h.aparc.stats files from recon-all, the 4th column(gray matter volume) of lh-precuneus and rh-precuneus are 5928 and 6125 respectively. I am confused because I thought the number of PET voxels should be equal to the number of GM voxels in the ROI?
Also, for output files such as gtm.nii.gz or nopvc.nii.gz, what programs can I open them with? It doesn't seem it is openned with mricron or gedit.
Thank you again in adavnce for your help.
Best,
Subin
________________________________ 보낸 사람: Douglas N Greve greve@nmr.mgh.harvard.edu 대신 freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu 보낸 날짜: 2016년 7월 8일 금요일 오전 2:53:31 받는 사람: freesurfer@nmr.mgh.harvard.edu 제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6
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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