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 <[email protected]> 대신 [email protected] <[email protected]> 보낸 날짜: 2016년 7월 8일 금요일 오전 2:53:31 받는 사람: [email protected] 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: > > > 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/[email protected]/msg43435.html) > <https://www.mail-archive.com/[email protected]/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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] 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.
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