Re: [Freesurfer] PVE correction tool on Freesurfer 6

2016-07-20 Thread Lee Subin Kristine
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 num

Re: [Freesurfer] PVE correction tool on Freesurfer 6

2016-07-18 Thread Douglas Greve

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> 대신 
freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu>

*보낸 날짜:* 2016년 7월 19일 화요일 오전 1:59:46
*받는 사람:* 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> 대신
> freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@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:
> >
> >
> > 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 thi

Re: [Freesurfer] PVE correction tool on Freesurfer 6

2016-07-18 Thread Lee Subin Kristine
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> 대신 
freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
보낸 날짜: 2016년 7월 19일 화요일 오전 1:59:46
받는 사람: 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> 대신
> freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@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:
> >
> >
> > 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 apa

Re: [Freesurfer] PVE correction tool on Freesurfer 6

2016-07-18 Thread Douglas N Greve


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> 대신 
> freesurfer-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@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:
> >
> >
> > 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.st

Re: [Freesurfer] PVE correction tool on Freesurfer 6

2016-07-12 Thread Lee Subin Kristine
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 <gr...@nmr.mgh.harvard.edu> 대신 
freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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:
>
>
> 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
>
>
>
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--
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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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
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Re: [Freesurfer] PVE correction tool on Freesurfer 6

2016-07-07 Thread Douglas N Greve
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) 
> 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
>
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
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/

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[Freesurfer] PVE correction tool on Freesurfer 6

2016-06-26 Thread Lee Subin Kristine
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)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

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