Hi Doug,
Thanks for your help! For your response to question #1 from my previous email(copied below), then if all PET images were smoothed so that they all have a uniform resolution of 8mm FWHM, would I put 8 for the psf flag? > 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. > In theory you need the FWHM for each scanner. The FWHM can also change depending upon recon method and parameters and even the ligand used. If you get it about right, probably it will be close enough. Also, for the second question (copied below), then does setting it to .01 mean maximum sensitivity to gray matter in each PET voxel, and thus this is the recommended threshold for the most accurate resutls? > (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? > You must enter a threshold. When Muller-Gartner is implemented, there are two stages: (1) orthogonalization (subtracting out non-GM) and (2) rescaling. In the rescaling step, each voxel is divided by the fraction of GM in that voxel. If that fraction is 0, then you will get an error. If it is close to 0, you can get extreme noise amplification in that voxel. Setting it to .01 requires that a voxel have at least 1% GM to be rescaled, otherwise the voxel is set to 0. Best, Subin ________________________________ 보낸 사람: Douglas Greve <gr...@nmr.mgh.harvard.edu> 대신 freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> 보낸 날짜: 2016년 7월 19일 화요일 오전 10:28:42 받는 사람: freesurfer@nmr.mgh.harvard.edu 제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6 the response is in the body f the mail On 7/18/16 9:27 PM, Lee Subin Kristine wrote: Hi Doug, It seems that the email reply you just sent to me was empty. Could you please check your email message again? Thank you as always, Subin ________________________________ 보낸 사람: Douglas N Greve <gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu> 대신 freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 보낸 날짜: 2016년 7월 19일 화요일 오전 1:59:46 받는 사람: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6 On 07/12/2016 11:03 PM, Lee Subin Kristine wrote: > > 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. > In theory you need the FWHM for each scanner. The FWHM can also change depending upon recon method and parameters and even the ligand used. If you get it about right, probably it will be close enough. > > (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? > You must enter a threshold. When Muller-Gartner is implemented, there are two stages: (1) orthogonalization (subtracting out non-GM) and (2) rescaling. In the rescaling step, each voxel is divided by the fraction of GM in that voxel. If that fraction is 0, then you will get an error. If it is close to 0, you can get extreme noise amplification in that voxel. Setting it to .01 requires that a voxel have at least 1% GM to be rescaled, otherwise the voxel is set to 0. > > > 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? > You need to scale by the size of the PET voxel. > > 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. > They are nifti files, though you probably don't want to use a nifit viewer. You can load them into matlab with MRIread('file.nii.gz') > > Thank you again in adavnce for your help. > > > Best, > > Subin > > ------------------------------------------------------------------------ > *보낸 사람:* Douglas N Greve > <gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu> 대신 > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > *보낸 날짜:* 2016년 7월 8일 금요일 오전 2:53:31 > *받는 사람:* freesurfer@nmr.mgh.harvard.edu<mailto: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: > > > > > > 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<mailto: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<mailto: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<http://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. > > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu<mailto: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<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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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