Dear Freesurfer experts!
I am currently working on PET analysis using FS
I coregistered my PET with the processed MR using bbregister, transfered it to a surface using mri_vol2surf and now createt an overlay in freeview with the lh.inflated and used the labels from the lh.aparc.a2009s.annot file.
In freeview i get the corresponding BP value for each vertex now but is there a way to get a list of vertices with the corresponding BP value and the corresponding ROI this vertex belongs to? Or is there a better to do this analyis?
Many thanks in advance!
Benjamin
If you want to use partial volume correction, then you are better off using mri_gtmpvc with the bbr registration, something like
1. To start, run
gtmseg --s subject
This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV).
2. You'd then register the PET to the anatomical with bbregister (probably with --t2 weighting). Make sure to save the output as an LTA (--lta). I usually use the mean TAC as the input. You can do this in parallel with #1.
3. You'd then run mri_gtmpvc, something like
mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg gtmseg.mgz --reg reg.lta --default-seg-merge --o gtmpvc.output
PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. By default, this will scale by pons. The output will be gtm.stats.dat and gtm.nii.gz. They both basically have the same information. gtm.stats.dat is an easy to read text file. Where each row is an ROI, something like:
9 17 Left-Hippocampus subcort_gm 473 174.083 1.406 0.1216
9 = nineth row 17 = index for RO Left-Hippocampus = name of ROI subcort_gm = tissue class 473 = number of PET voxels in the ROI 174 = variance reduction factor for ROI (based on GLM/SGTM) 1.406 = PVC uptake of ROI relative to Pons 0.1216 = resdiual varaince across voxels in the ROI
gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value is the PVC uptake of ROI relative to Pons. These can easily be concatenated together (mri_concat) and used as input to mri_glmfit for group analysis.
On 01/08/2016 04:22 AM, Benjamin Spurny wrote:
Dear Freesurfer experts!
I am currently working on PET analysis using FS
I coregistered my PET with the processed MR using bbregister, transfered it to a surface using mri_vol2surf and now createt an overlay in freeview with the lh.inflated and used the labels from the lh.aparc.a2009s.annot file.
In freeview i get the corresponding BP value for each vertex now but is there a way to get a list of vertices with the corresponding BP value and the corresponding ROI this vertex belongs to? Or is there a better to do this analyis?
Many thanks in advance!
Benjamin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Doug,
I have used the gtmseg with --keep-cc flag and the corresponding ctab files showed the labels but the mri_gtmpvc step failed. **** Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check **** My objective is to use the combination of all CC's as a reference region and obtain the PVC results, which would be listed in gtm.stats.dat
Also, I read in the previous email discussions that the default ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with another ROI as a reference region, would it be OK take a ratio of the ROI's in gtm.stats.dat table.
Thanks, Pradeep
On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
If you want to use partial volume correction, then you are better off using mri_gtmpvc with the bbr registration, something like
- To start, run
gtmseg --s subject
This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV).
- You'd then register the PET to the anatomical with bbregister
(probably with --t2 weighting). Make sure to save the output as an LTA (--lta). I usually use the mean TAC as the input. You can do this in parallel with #1.
- You'd then run mri_gtmpvc, something like
mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg gtmseg.mgz --reg reg.lta --default-seg-merge --o gtmpvc.output
PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. By default, this will scale by pons. The output will be gtm.stats.dat and gtm.nii.gz. They both basically have the same information. gtm.stats.dat is an easy to read text file. Where each row is an ROI, something like:
9 17 Left-Hippocampus subcort_gm 473 174.083 1.406 0.1216
9 = nineth row 17 = index for RO Left-Hippocampus = name of ROI subcort_gm = tissue class 473 = number of PET voxels in the ROI 174 = variance reduction factor for ROI (based on GLM/SGTM) 1.406 = PVC uptake of ROI relative to Pons 0.1216 = resdiual varaince across voxels in the ROI
gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value is the PVC uptake of ROI relative to Pons. These can easily be concatenated together (mri_concat) and used as input to mri_glmfit for group analysis.
On 01/08/2016 04:22 AM, Benjamin Spurny wrote:
Dear Freesurfer experts!
I am currently working on PET analysis using FS
I coregistered my PET with the processed MR using bbregister, transfered it to a surface using mri_vol2surf and now createt an overlay in freeview with the lh.inflated and used the labels from the lh.aparc.a2009s.annot file.
In freeview i get the corresponding BP value for each vertex now but is there a way to get a list of vertices with the corresponding BP value and the corresponding ROI this vertex belongs to? Or is there a better to do this analyis?
Many thanks in advance!
Benjamin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
Freesurfer mailing list 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.
On 01/28/2016 06:50 PM, Pradeep wrote:
Hello Doug,
I have used the gtmseg with --keep-cc flag and the corresponding ctab files showed the labels but the mri_gtmpvc step failed.
Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
What is your mri_gtmpvc command line? What is the rest of the terminal output?
My objective is to use the combination of all CC's as a reference region and obtain the PVC results, which would be listed in gtm.stats.dat
It will be best to combine them when running mri_gtmpvc using --replace, eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 this will cause all segments of the CC to appear to be a single segment (251).
Also, I read in the previous email discussions that the default ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with another ROI as a reference region, would it be OK take a ratio of the ROI's in gtm.stats.dat table.
Yes, or you can spec the new region, eg --rescale 251
Thanks, Pradeep
On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you want to use partial volume correction, then you are better off using mri_gtmpvc with the bbr registration, something like 1. To start, run gtmseg --s subject This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV). 2. You'd then register the PET to the anatomical with bbregister (probably with --t2 weighting). Make sure to save the output as an LTA (--lta). I usually use the mean TAC as the input. You can do this in parallel with #1. 3. You'd then run mri_gtmpvc, something like mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg gtmseg.mgz --reg reg.lta --default-seg-merge --o gtmpvc.output PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. By default, this will scale by pons. The output will be gtm.stats.dat and gtm.nii.gz. They both basically have the same information. gtm.stats.dat is an easy to read text file. Where each row is an ROI, something like: 9 17 Left-Hippocampus subcort_gm 473 174.083 1.406 0.1216 9 = nineth row 17 = index for RO Left-Hippocampus = name of ROI subcort_gm = tissue class 473 = number of PET voxels in the ROI 174 = variance reduction factor for ROI (based on GLM/SGTM) 1.406 = PVC uptake of ROI relative to Pons 0.1216 = resdiual varaince across voxels in the ROI gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value is the PVC uptake of ROI relative to Pons. These can easily be concatenated together (mri_concat) and used as input to mri_glmfit for group analysis. On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > Dear Freesurfer experts! > > I am currently working on PET analysis using FS > > I coregistered my PET with the processed MR using bbregister, > transfered it to a surface using mri_vol2surf > and now createt an overlay in freeview with the lh.inflated and used the > labels from the lh.aparc.a2009s.annot file. > > In freeview i get the corresponding BP value for each vertex now but > is there a way to get a list of vertices with the corresponding BP value > and the corresponding ROI this vertex belongs to? > Or is there a better to do this analyis? > > Many thanks in advance! > > Benjamin > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you for the response.
Here is my full command log with error
$gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc
$ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o gtmpvccc.output Loading input t12pet.nii.gz done loading input 1 frames
$Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ setenv SUBJECTS_DIR /analysis/software_test/fs6pvc cd /analysis/software_test/fs6pvc/******/mri mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o gtmpvccc.output sysname Linux hostname server machine x86_64 user user vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 9 avail.processors, using 9 Creating output directory gtmpvccc.output Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
Thanks, Pradeep
On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
On 01/28/2016 06:50 PM, Pradeep wrote:
Hello Doug,
I have used the gtmseg with --keep-cc flag and the corresponding ctab files showed the labels but the mri_gtmpvc step failed.
Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
What is your mri_gtmpvc command line? What is the rest of the terminal output?
My objective is to use the combination of all CC's as a reference region and obtain the PVC results, which would be listed in gtm.stats.dat
It will be best to combine them when running mri_gtmpvc using --replace, eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 this will cause all segments of the CC to appear to be a single segment (251).
Also, I read in the previous email discussions that the default ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with another ROI as a reference region, would it be OK take a ratio of the ROI's in gtm.stats.dat table.
Yes, or you can spec the new region, eg --rescale 251
Thanks, Pradeep
On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you want to use partial volume correction, then you are better off using mri_gtmpvc with the bbr registration, something like 1. To start, run gtmseg --s subject This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV). 2. You'd then register the PET to the anatomical with bbregister (probably with --t2 weighting). Make sure to save the output as anLTA
(--lta). I usually use the mean TAC as the input. You can do this in parallel with #1. 3. You'd then run mri_gtmpvc, something like mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg gtmseg.mgz --reg reg.lta --default-seg-merge --o gtmpvc.output PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. By default, this will scale by pons. The output will be gtm.stats.dat and gtm.nii.gz. They both basically have the same information. gtm.stats.dat is an easy to read text file. Where each row is an ROI, something like: 9 17 Left-Hippocampus subcort_gm 473 174.083 1.406 0.1216 9 = nineth row 17 = index for RO Left-Hippocampus = name of ROI subcort_gm = tissue class 473 = number of PET voxels in the ROI 174 = variance reduction factor for ROI (based on GLM/SGTM) 1.406 = PVC uptake of ROI relative to Pons 0.1216 = resdiual varaince across voxels in the ROI gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value is the PVC uptake of ROI relative to Pons. These can easily be concatenated together (mri_concat) and used as input to mri_glmfit for group analysis. On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > Dear Freesurfer experts! > > I am currently working on PET analysis using FS > > I coregistered my PET with the processed MR using bbregister, > transfered it to a surface using mri_vol2surf > and now createt an overlay in freeview with the lh.inflated and used the > labels from the lh.aparc.a2009s.annot file. > > In freeview i get the corresponding BP value for each vertex nowbut
> is there a way to get a list of vertices with the corresponding BP value > and the corresponding ROI this vertex belongs to? > Or is there a better to do this analyis? > > Many thanks in advance! > > Benjamin > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think I see the problem. When you run gtmseg, you need to add --keep-cc. You can rerun it using the previous command line, but add --keep-cc and --no-xcerseg. The second option tells it not to redo the extracerebral segmentation (which won't change with CC)
On 01/29/2016 11:21 AM, Pradeep wrote:
Thank you for the response.
Here is my full command log with error
$gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc
$ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o gtmpvccc.output Loading input t12pet.nii.gz done loading input 1 frames
$Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ setenv SUBJECTS_DIR /analysis/software_test/fs6pvc cd /analysis/software_test/fs6pvc/******/mri mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o gtmpvccc.output sysname Linux hostname server machine x86_64 user user vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 9 avail.processors, using 9 Creating output directory gtmpvccc.output Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
Thanks, Pradeep
On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 01/28/2016 06:50 PM, Pradeep wrote: > Hello Doug, > > I have used the gtmseg with --keep-cc flag and the corresponding ctab > files showed the labels but the mri_gtmpvc step failed. > **** > Loading seg for gtm gtmseg.mgz > Loading seg ctab gtmseg.ctab > Reading gtmseg.lta > Replacing 18 > ERROR: CheckSegTissueType() no entry for seg 192 > Failed tissue type check > **** What is your mri_gtmpvc command line? What is the rest of the terminal output? > My objective is to use the combination of all CC's as a reference > region and obtain the PVC results, which would be listed in gtm.stats.dat It will be best to combine them when running mri_gtmpvc using --replace, eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 this will cause all segments of the CC to appear to be a single segment (251). > > Also, I read in the previous email discussions that the default > ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with > another ROI as a reference region, > would it be OK take a ratio of the ROI's in gtm.stats.dat table. Yes, or you can spec the new region, eg --rescale 251 > > Thanks, > Pradeep > > On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > If you want to use partial volume correction, then you are better off > using mri_gtmpvc with the bbr registration, something like > > 1. To start, run > > gtmseg --s subject > > This will take a couple of hours and produces some files needed > for GTM > PVC (which is used for GTM, MG, RBV). > > 2. You'd then register the PET to the anatomical with bbregister > (probably with --t2 weighting). Make sure to save the output as an LTA > (--lta). I usually use the mean TAC as the input. You can do this in > parallel with #1. > > 3. You'd then run mri_gtmpvc, something like > > mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg > gtmseg.mgz > --reg reg.lta --default-seg-merge --o gtmpvc.output > > PSF is the point-spread FWHM of the scanner; reg.lta is the > registration from #2. By default, this will scale by pons. The output > will be gtm.stats.dat and gtm.nii.gz. They both basically have the > same information. gtm.stats.dat is an easy to read text file. Where > each row is an ROI, something like: > > 9 17 Left-Hippocampus subcort_gm 473 > 174.083 1.406 0.1216 > > 9 = nineth row > 17 = index for RO > Left-Hippocampus = name of ROI > subcort_gm = tissue class > 473 = number of PET voxels in the ROI > 174 = variance reduction factor for ROI (based on GLM/SGTM) > 1.406 = PVC uptake of ROI relative to Pons > 0.1216 = resdiual varaince across voxels in the ROI > > gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value > is the PVC uptake of ROI relative to Pons. These can easily be > concatenated together (mri_concat) and used as input to mri_glmfit > for group analysis. > > > > > On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > > Dear Freesurfer experts! > > > > I am currently working on PET analysis using FS > > > > I coregistered my PET with the processed MR using bbregister, > > transfered it to a surface using mri_vol2surf > > and now createt an overlay in freeview with the lh.inflated and > used the > > labels from the lh.aparc.a2009s.annot file. > > > > In freeview i get the corresponding BP value for each vertex now but > > is there a way to get a list of vertices with the corresponding > BP value > > and the corresponding ROI this vertex belongs to? > > Or is there a better to do this analyis? > > > > Many thanks in advance! > > > > Benjamin > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> <mailto: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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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
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Unfortunately, that did not fix the problem.
Here is what I did 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg # no errors
3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output Loading input t12pet.nii.gz done loading input 1 frames ERROR: item 251 appears as both source and target seg id in replacement list
$Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ setenv SUBJECTS_DIR /analysis/software_test/fs6pvc cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output sysname Linux hostname machine x86_64 user vgthresh 0.001000 nReplace 22 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 9 avail.processors, using 9 Creating output directory gtmpvcrcc.output Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 22 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
Thank you for looking into this, Pradeep
On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
I think I see the problem. When you run gtmseg, you need to add --keep-cc. You can rerun it using the previous command line, but add --keep-cc and --no-xcerseg. The second option tells it not to redo the extracerebral segmentation (which won't change with CC)
On 01/29/2016 11:21 AM, Pradeep wrote:
Thank you for the response.
Here is my full command log with error
$gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc
$ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o gtmpvccc.output Loading input t12pet.nii.gz done loading input 1 frames
$Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ setenv SUBJECTS_DIR /analysis/software_test/fs6pvc cd /analysis/software_test/fs6pvc/******/mri mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o gtmpvccc.output sysname Linux hostname server machine x86_64 user user vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 9 avail.processors, using 9 Creating output directory gtmpvccc.output Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
Thanks, Pradeep
On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 01/28/2016 06:50 PM, Pradeep wrote: > Hello Doug, > > I have used the gtmseg with --keep-cc flag and the corresponding ctab > files showed the labels but the mri_gtmpvc step failed. > **** > Loading seg for gtm gtmseg.mgz > Loading seg ctab gtmseg.ctab > Reading gtmseg.lta > Replacing 18 > ERROR: CheckSegTissueType() no entry for seg 192 > Failed tissue type check > **** What is your mri_gtmpvc command line? What is the rest of theterminal
output? > My objective is to use the combination of all CC's as a reference > region and obtain the PVC results, which would be listed in gtm.stats.dat It will be best to combine them when running mri_gtmpvc using --replace, eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 this will cause all segments of the CC to appear to be a single segment (251). > > Also, I read in the previous email discussions that the default > ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVRwith
> another ROI as a reference region, > would it be OK take a ratio of the ROI's in gtm.stats.dat table. Yes, or you can spec the new region, eg --rescale 251 > > Thanks, > Pradeep > > On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > If you want to use partial volume correction, then you are better off > using mri_gtmpvc with the bbr registration, something like > > 1. To start, run > > gtmseg --s subject > > This will take a couple of hours and produces some files needed > for GTM > PVC (which is used for GTM, MG, RBV). > > 2. You'd then register the PET to the anatomical withbbregister
> (probably with --t2 weighting). Make sure to save the output as an LTA > (--lta). I usually use the mean TAC as the input. You can do this in > parallel with #1. > > 3. You'd then run mri_gtmpvc, something like > > mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg > gtmseg.mgz > --reg reg.lta --default-seg-merge --o gtmpvc.output > > PSF is the point-spread FWHM of the scanner; reg.lta is the > registration from #2. By default, this will scale by pons. The output > will be gtm.stats.dat and gtm.nii.gz. They both basically have the > same information. gtm.stats.dat is an easy to read text file. Where > each row is an ROI, something like: > > 9 17 Left-Hippocampus subcort_gm 473 > 174.083 1.406 0.1216 > > 9 = nineth row > 17 = index for RO > Left-Hippocampus = name of ROI > subcort_gm = tissue class > 473 = number of PET voxels in the ROI > 174 = variance reduction factor for ROI (based on GLM/SGTM) > 1.406 = PVC uptake of ROI relative to Pons > 0.1216 = resdiual varaince across voxels in the ROI > > gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value > is the PVC uptake of ROI relative to Pons. These can easily be > concatenated together (mri_concat) and used as input to mri_glmfit > for group analysis. > > > > > On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > > Dear Freesurfer experts! > > > > I am currently working on PET analysis using FS > > > > I coregistered my PET with the processed MR using bbregister, > > transfered it to a surface using mri_vol2surf > > and now createt an overlay in freeview with the lh.inflated and > used the > > labels from the lh.aparc.a2009s.annot file. > > > > In freeview i get the corresponding BP value for each vertex now but > > is there a way to get a list of vertices with the corresponding > BP value > > and the corresponding ROI this vertex belongs to? > > Or is there a better to do this analyis? > > > > Many thanks in advance! > > > > Benjamin > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> <mailto: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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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>
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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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The problem is that --default-seg-merge merges the CC with WM, so you can't use that option, which means that you'll have to specify the rest of the default seg merge manually. You can do this with more --replace args or you can create a file. If you've been able to run mri_gtmpvc without the current replace, then it will create a replacement file in the aux folder. Get that, remove the 251 entry, and change the 252-255 entries to point to 251
On 01/29/2016 02:12 PM, Pradeep wrote:
Unfortunately, that did not fix the problem.
Here is what I did 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg # no errors
3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output Loading input t12pet.nii.gz done loading input 1 frames ERROR: item 251 appears as both source and target seg id in replacement list
$Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ setenv SUBJECTS_DIR /analysis/software_test/fs6pvc cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output sysname Linux hostname machine x86_64 user vgthresh 0.001000 nReplace 22 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 9 avail.processors, using 9 Creating output directory gtmpvcrcc.output Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 22 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
Thank you for looking into this, Pradeep
On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think I see the problem. When you run gtmseg, you need to add --keep-cc. You can rerun it using the previous command line, but add --keep-cc and --no-xcerseg. The second option tells it not to redo the extracerebral segmentation (which won't change with CC) On 01/29/2016 11:21 AM, Pradeep wrote: > Thank you for the response. > > Here is my full command log with error > > > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc > > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > gtmpvccc.output > Loading input t12pet.nii.gz > done loading input 1 frames > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc > cd /analysis/software_test/fs6pvc/******/mri > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > gtmpvccc.output > sysname Linux > hostname server > machine x86_64 > user user > vgthresh 0.001000 > nReplace 18 > 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 9 avail.processors, using 9 > Creating output directory gtmpvccc.output > Loading seg for gtm gtmseg.mgz > Loading seg ctab gtmseg.ctab > Reading gtmseg.lta > Replacing 18 > ERROR: CheckSegTissueType() no entry for seg 192 > Failed tissue type check > > > Thanks, > Pradeep > > > On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > On 01/28/2016 06:50 PM, Pradeep wrote: > > Hello Doug, > > > > I have used the gtmseg with --keep-cc flag and the > corresponding ctab > > files showed the labels but the mri_gtmpvc step failed. > > **** > > Loading seg for gtm gtmseg.mgz > > Loading seg ctab gtmseg.ctab > > Reading gtmseg.lta > > Replacing 18 > > ERROR: CheckSegTissueType() no entry for seg 192 > > Failed tissue type check > > **** > What is your mri_gtmpvc command line? What is the rest of the terminal > output? > > My objective is to use the combination of all CC's as a reference > > region and obtain the PVC results, which would be listed in > gtm.stats.dat > It will be best to combine them when running mri_gtmpvc using > --replace, > eg, --replace 252 251 --replace 253 251 --replace 254 251 > --replace 255 251 > this will cause all segments of the CC to appear to be a single > segment > (251). > > > > Also, I read in the previous email discussions that the default > > ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with > > another ROI as a reference region, > > would it be OK take a ratio of the ROI's in gtm.stats.dat table. > Yes, or you can spec the new region, eg --rescale 251 > > > > Thanks, > > Pradeep > > > > On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > If you want to use partial volume correction, then you are > better off > > using mri_gtmpvc with the bbr registration, something like > > > > 1. To start, run > > > > gtmseg --s subject > > > > This will take a couple of hours and produces some files needed > > for GTM > > PVC (which is used for GTM, MG, RBV). > > > > 2. You'd then register the PET to the anatomical with bbregister > > (probably with --t2 weighting). Make sure to save the output > as an LTA > > (--lta). I usually use the mean TAC as the input. You can do > this in > > parallel with #1. > > > > 3. You'd then run mri_gtmpvc, something like > > > > mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg > > gtmseg.mgz > > --reg reg.lta --default-seg-merge --o gtmpvc.output > > > > PSF is the point-spread FWHM of the scanner; reg.lta is the > > registration from #2. By default, this will scale by pons. > The output > > will be gtm.stats.dat and gtm.nii.gz. They both basically > have the > > same information. gtm.stats.dat is an easy to read text > file. Where > > each row is an ROI, something like: > > > > 9 17 Left-Hippocampus subcort_gm 473 > > 174.083 1.406 0.1216 > > > > 9 = nineth row > > 17 = index for RO > > Left-Hippocampus = name of ROI > > subcort_gm = tissue class > > 473 = number of PET voxels in the ROI > > 174 = variance reduction factor for ROI (based on GLM/SGTM) > > 1.406 = PVC uptake of ROI relative to Pons > > 0.1216 = resdiual varaince across voxels in the ROI > > > > gtm.nii.gz is a nifti file with each "voxel" being an ROI. > The value > > is the PVC uptake of ROI relative to Pons. These can easily be > > concatenated together (mri_concat) and used as input to > mri_glmfit > > for group analysis. > > > > > > > > > > On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > > > Dear Freesurfer experts! > > > > > > I am currently working on PET analysis using FS > > > > > > I coregistered my PET with the processed MR using bbregister, > > > transfered it to a surface using mri_vol2surf > > > and now createt an overlay in freeview with the > lh.inflated and > > used the > > > labels from the lh.aparc.a2009s.annot file. > > > > > > In freeview i get the corresponding BP value for each > vertex now but > > > is there a way to get a list of vertices with the > corresponding > > BP value > > > and the corresponding ROI this vertex belongs to? > > > Or is there a better to do this analyis? > > > > > > Many thanks in advance! > > > > > > Benjamin > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://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> > > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto: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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> <mailto: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 -- Douglas N. 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It worked! Thank you! mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --replace-file seg.replace251.list --rescale 251 --mgx 0.01 --o gtmpvcRcc.output
On Fri, Jan 29, 2016 at 12:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
The problem is that --default-seg-merge merges the CC with WM, so you can't use that option, which means that you'll have to specify the rest of the default seg merge manually. You can do this with more --replace args or you can create a file. If you've been able to run mri_gtmpvc without the current replace, then it will create a replacement file in the aux folder. Get that, remove the 251 entry, and change the 252-255 entries to point to 251
On 01/29/2016 02:12 PM, Pradeep wrote:
Unfortunately, that did not fix the problem.
Here is what I did 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg # no errors
3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output Loading input t12pet.nii.gz done loading input 1 frames ERROR: item 251 appears as both source and target seg id in replacement list
$Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ setenv SUBJECTS_DIR /analysis/software_test/fs6pvc cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output sysname Linux hostname machine x86_64 user vgthresh 0.001000 nReplace 22 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 9 avail.processors, using 9 Creating output directory gtmpvcrcc.output Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 22 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
Thank you for looking into this, Pradeep
On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think I see the problem. When you run gtmseg, you need to add --keep-cc. You can rerun it using the previous command line, but add --keep-cc and --no-xcerseg. The second option tells it not to redothe
extracerebral segmentation (which won't change with CC) On 01/29/2016 11:21 AM, Pradeep wrote: > Thank you for the response. > > Here is my full command log with error > > > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc > > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > gtmpvccc.output > Loading input t12pet.nii.gz > done loading input 1 frames > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc > cd /analysis/software_test/fs6pvc/******/mri > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > gtmpvccc.output > sysname Linux > hostname server > machine x86_64 > user user > vgthresh 0.001000 > nReplace 18 > 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 9 avail.processors, using 9 > Creating output directory gtmpvccc.output > Loading seg for gtm gtmseg.mgz > Loading seg ctab gtmseg.ctab > Reading gtmseg.lta > Replacing 18 > ERROR: CheckSegTissueType() no entry for seg 192 > Failed tissue type check > > > Thanks, > Pradeep > > > On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > On 01/28/2016 06:50 PM, Pradeep wrote: > > Hello Doug, > > > > I have used the gtmseg with --keep-cc flag and the > corresponding ctab > > files showed the labels but the mri_gtmpvc step failed. > > **** > > Loading seg for gtm gtmseg.mgz > > Loading seg ctab gtmseg.ctab > > Reading gtmseg.lta > > Replacing 18 > > ERROR: CheckSegTissueType() no entry for seg 192 > > Failed tissue type check > > **** > What is your mri_gtmpvc command line? What is the rest of the terminal > output? > > My objective is to use the combination of all CC's as a reference > > region and obtain the PVC results, which would be listed in > gtm.stats.dat > It will be best to combine them when running mri_gtmpvc using > --replace, > eg, --replace 252 251 --replace 253 251 --replace 254 251 > --replace 255 251 > this will cause all segments of the CC to appear to be a single > segment > (251). > > > > Also, I read in the previous email discussions that the default > > ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with > > another ROI as a reference region, > > would it be OK take a ratio of the ROI's in gtm.stats.dat table. > Yes, or you can spec the new region, eg --rescale 251 > > > > Thanks, > > Pradeep > > > > On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > If you want to use partial volume correction, then youare
> better off > > using mri_gtmpvc with the bbr registration, somethinglike
> > > > 1. To start, run > > > > gtmseg --s subject > > > > This will take a couple of hours and produces some files needed > > for GTM > > PVC (which is used for GTM, MG, RBV). > > > > 2. You'd then register the PET to the anatomical with bbregister > > (probably with --t2 weighting). Make sure to save the output > as an LTA > > (--lta). I usually use the mean TAC as the input. You can do > this in > > parallel with #1. > > > > 3. You'd then run mri_gtmpvc, something like > > > > mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg > > gtmseg.mgz > > --reg reg.lta --default-seg-merge --o gtmpvc.output > > > > PSF is the point-spread FWHM of the scanner; reg.lta is the > > registration from #2. By default, this will scale bypons.
> The output > > will be gtm.stats.dat and gtm.nii.gz. They both basically > have the > > same information. gtm.stats.dat is an easy to read text > file. Where > > each row is an ROI, something like: > > > > 9 17 Left-Hippocampus subcort_gm 473 > > 174.083 1.406 0.1216 > > > > 9 = nineth row > > 17 = index for RO > > Left-Hippocampus = name of ROI > > subcort_gm = tissue class > > 473 = number of PET voxels in the ROI > > 174 = variance reduction factor for ROI (based on GLM/SGTM) > > 1.406 = PVC uptake of ROI relative to Pons > > 0.1216 = resdiual varaince across voxels in the ROI > > > > gtm.nii.gz is a nifti file with each "voxel" being anROI.
> The value > > is the PVC uptake of ROI relative to Pons. These can easily be > > concatenated together (mri_concat) and used as input to > mri_glmfit > > for group analysis. > > > > > > > > > > On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > > > Dear Freesurfer experts! > > > > > > I am currently working on PET analysis using FS > > > > > > I coregistered my PET with the processed MR using bbregister, > > > transfered it to a surface using mri_vol2surf > > > and now createt an overlay in freeview with the > lh.inflated and > > used the > > > labels from the lh.aparc.a2009s.annot file. > > > > > > In freeview i get the corresponding BP value for each > vertex now but > > > is there a way to get a list of vertices with the > corresponding > > BP value > > > and the corresponding ROI this vertex belongs to? > > > Or is there a better to do this analyis? > > > > > > Many thanks in advance! > > > > > > Benjamin > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 tel:617-724-2358>
> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://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> > > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto: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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> <mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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>
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Hello Doug,
I was wondering if there is a flag in the command to obtain the SUVRs for the same ROIs with out partial volume correction so that it would be easier to compare.
Thanks, Pradeep
On Fri, Jan 29, 2016 at 1:30 PM, Pradeep tpradeep@gmail.com wrote:
It worked! Thank you! mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --replace-file seg.replace251.list --rescale 251 --mgx 0.01 --o gtmpvcRcc.output
On Fri, Jan 29, 2016 at 12:23 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
The problem is that --default-seg-merge merges the CC with WM, so you can't use that option, which means that you'll have to specify the rest of the default seg merge manually. You can do this with more --replace args or you can create a file. If you've been able to run mri_gtmpvc without the current replace, then it will create a replacement file in the aux folder. Get that, remove the 251 entry, and change the 252-255 entries to point to 251
On 01/29/2016 02:12 PM, Pradeep wrote:
Unfortunately, that did not fix the problem.
Here is what I did 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg # no errors
3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output Loading input t12pet.nii.gz done loading input 1 frames ERROR: item 251 appears as both source and target seg id in replacement list
$Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ setenv SUBJECTS_DIR /analysis/software_test/fs6pvc cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output sysname Linux hostname machine x86_64 user vgthresh 0.001000 nReplace 22 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 9 avail.processors, using 9 Creating output directory gtmpvcrcc.output Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 22 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
Thank you for looking into this, Pradeep
On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think I see the problem. When you run gtmseg, you need to add --keep-cc. You can rerun it using the previous command line, but add --keep-cc and --no-xcerseg. The second option tells it not to redothe
extracerebral segmentation (which won't change with CC) On 01/29/2016 11:21 AM, Pradeep wrote: > Thank you for the response. > > Here is my full command log with error > > > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc > > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01--seg
> gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > gtmpvccc.output > Loading input t12pet.nii.gz > done loading input 1 frames > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc > cd /analysis/software_test/fs6pvc/******/mri > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > gtmpvccc.output > sysname Linux > hostname server > machine x86_64 > user user > vgthresh 0.001000 > nReplace 18 > 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 9 avail.processors, using 9 > Creating output directory gtmpvccc.output > Loading seg for gtm gtmseg.mgz > Loading seg ctab gtmseg.ctab > Reading gtmseg.lta > Replacing 18 > ERROR: CheckSegTissueType() no entry for seg 192 > Failed tissue type check > > > Thanks, > Pradeep > > > On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > On 01/28/2016 06:50 PM, Pradeep wrote: > > Hello Doug, > > > > I have used the gtmseg with --keep-cc flag and the > corresponding ctab > > files showed the labels but the mri_gtmpvc step failed. > > **** > > Loading seg for gtm gtmseg.mgz > > Loading seg ctab gtmseg.ctab > > Reading gtmseg.lta > > Replacing 18 > > ERROR: CheckSegTissueType() no entry for seg 192 > > Failed tissue type check > > **** > What is your mri_gtmpvc command line? What is the rest of the terminal > output? > > My objective is to use the combination of all CC's as a reference > > region and obtain the PVC results, which would be listed in > gtm.stats.dat > It will be best to combine them when running mri_gtmpvc using > --replace, > eg, --replace 252 251 --replace 253 251 --replace 254 251 > --replace 255 251 > this will cause all segments of the CC to appear to be asingle
> segment > (251). > > > > Also, I read in the previous email discussions that the default > > ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with > > another ROI as a reference region, > > would it be OK take a ratio of the ROI's in gtm.stats.dat table. > Yes, or you can spec the new region, eg --rescale 251 > > > > Thanks, > > Pradeep > > > > On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > If you want to use partial volume correction, then youare
> better off > > using mri_gtmpvc with the bbr registration, somethinglike
> > > > 1. To start, run > > > > gtmseg --s subject > > > > This will take a couple of hours and produces some files needed > > for GTM > > PVC (which is used for GTM, MG, RBV). > > > > 2. You'd then register the PET to the anatomical with bbregister > > (probably with --t2 weighting). Make sure to save the output > as an LTA > > (--lta). I usually use the mean TAC as the input. You can do > this in > > parallel with #1. > > > > 3. You'd then run mri_gtmpvc, something like > > > > mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg > > gtmseg.mgz > > --reg reg.lta --default-seg-merge --o gtmpvc.output > > > > PSF is the point-spread FWHM of the scanner; reg.lta is the > > registration from #2. By default, this will scale bypons.
> The output > > will be gtm.stats.dat and gtm.nii.gz. They bothbasically
> have the > > same information. gtm.stats.dat is an easy to read text > file. Where > > each row is an ROI, something like: > > > > 9 17 Left-Hippocampus subcort_gm 473 > > 174.083 1.406 0.1216 > > > > 9 = nineth row > > 17 = index for RO > > Left-Hippocampus = name of ROI > > subcort_gm = tissue class > > 473 = number of PET voxels in the ROI > > 174 = variance reduction factor for ROI (based on GLM/SGTM) > > 1.406 = PVC uptake of ROI relative to Pons > > 0.1216 = resdiual varaince across voxels in the ROI > > > > gtm.nii.gz is a nifti file with each "voxel" being anROI.
> The value > > is the PVC uptake of ROI relative to Pons. These can easily be > > concatenated together (mri_concat) and used as input to > mri_glmfit > > for group analysis. > > > > > > > > > > On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > > > Dear Freesurfer experts! > > > > > > I am currently working on PET analysis using FS > > > > > > I coregistered my PET with the processed MR using bbregister, > > > transfered it to a surface using mri_vol2surf > > > and now createt an overlay in freeview with the > lh.inflated and > > used the > > > labels from the lh.aparc.a2009s.annot file. > > > > > > In freeview i get the corresponding BP value for each > vertex now but > > > is there a way to get a list of vertices with the > corresponding > > BP value > > > and the corresponding ROI this vertex belongs to? > > > Or is there a better to do this analyis? > > > > > > Many thanks in advance! > > > > > > Benjamin > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 tel:617-724-2358>
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No, not yet, though I recently had a need to do the same thing. It is pretty easy to do though. If you run mri_gtmpvc with --save-input, it will create a file called input.rescaled.nii.gz. Then you can run mri_segstats --i input.rescaled.nii.gz --seg aux/seg.nii.gz --ctab aux/seg.ctab --avgwfvol nopvc.nii.gz
nopvc.nii.gz will be the same size as gtm.nii.gz with the same order of ROIs. Not that the ROI used to rescale in the gtmpvc command (251 for you) will not have a value of 1.0 in the nopvc.nii.gz, so if you want to compare, then you'll need to rescale yourself.
On 02/24/2016 12:46 PM, Pradeep wrote:
Hello Doug,
I was wondering if there is a flag in the command to obtain the SUVRs for the same ROIs with out partial volume correction so that it would be easier to compare.
Thanks, Pradeep
On Fri, Jan 29, 2016 at 1:30 PM, Pradeep <tpradeep@gmail.com mailto:tpradeep@gmail.com> wrote:
It worked! Thank you! mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --replace-file seg.replace251.list --rescale 251 --mgx 0.01 --o gtmpvcRcc.output On Fri, Jan 29, 2016 at 12:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: The problem is that --default-seg-merge merges the CC with WM, so you can't use that option, which means that you'll have to specify the rest of the default seg merge manually. You can do this with more --replace args or you can create a file. If you've been able to run mri_gtmpvc without the current replace, then it will create a replacement file in the aux folder. Get that, remove the 251 entry, and change the 252-255 entries to point to 251 On 01/29/2016 02:12 PM, Pradeep wrote: > Unfortunately, that did not fix the problem. > > Here is what I did > 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors > 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg # no errors > > 3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o > gtmpvcrcc.output > Loading input t12pet.nii.gz > done loading input 1 frames > ERROR: item 251 appears as both source and target seg id in > replacement list > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc > cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o > gtmpvcrcc.output > sysname Linux > hostname > machine x86_64 > user > vgthresh 0.001000 > nReplace 22 > 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 9 avail.processors, using 9 > Creating output directory gtmpvcrcc.output > Loading seg for gtm gtmseg.mgz > Loading seg ctab gtmseg.ctab > Reading gtmseg.lta > Replacing 22 > ERROR: CheckSegTissueType() no entry for seg 192 > Failed tissue type check > > Thank you for looking into this, > Pradeep > > > On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > I think I see the problem. When you run gtmseg, you need to add > --keep-cc. You can rerun it using the previous command line, but add > --keep-cc and --no-xcerseg. The second option tells it not to redo the > extracerebral segmentation (which won't change with CC) > > On 01/29/2016 11:21 AM, Pradeep wrote: > > Thank you for the response. > > > > Here is my full command log with error > > > > > > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc > > > > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > > gtmpvccc.output > > Loading input t12pet.nii.gz > > done loading input 1 frames > > > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ > > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc > > cd /analysis/software_test/fs6pvc/******/mri > > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > > gtmpvccc.output > > sysname Linux > > hostname server > > machine x86_64 > > user user > > vgthresh 0.001000 > > nReplace 18 > > 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > > 9 avail.processors, using 9 > > Creating output directory gtmpvccc.output > > Loading seg for gtm gtmseg.mgz > > Loading seg ctab gtmseg.ctab > > Reading gtmseg.lta > > Replacing 18 > > ERROR: CheckSegTissueType() no entry for seg 192 > > Failed tissue type check > > > > > > Thanks, > > Pradeep > > > > > > On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > > > On 01/28/2016 06:50 PM, Pradeep wrote: > > > Hello Doug, > > > > > > I have used the gtmseg with --keep-cc flag and the > > corresponding ctab > > > files showed the labels but the mri_gtmpvc step failed. > > > **** > > > Loading seg for gtm gtmseg.mgz > > > Loading seg ctab gtmseg.ctab > > > Reading gtmseg.lta > > > Replacing 18 > > > ERROR: CheckSegTissueType() no entry for seg 192 > > > Failed tissue type check > > > **** > > What is your mri_gtmpvc command line? What is the rest of > the terminal > > output? > > > My objective is to use the combination of all CC's as a > reference > > > region and obtain the PVC results, which would be listed in > > gtm.stats.dat > > It will be best to combine them when running mri_gtmpvc using > > --replace, > > eg, --replace 252 251 --replace 253 251 --replace 254 251 > > --replace 255 251 > > this will cause all segments of the CC to appear to be a single > > segment > > (251). > > > > > > Also, I read in the previous email discussions that the > default > > > ref-region Pons is 'PVC'ed'. So if I want to calculate the > SUVR with > > > another ROI as a reference region, > > > would it be OK take a ratio of the ROI's in gtm.stats.dat > table. > > Yes, or you can spec the new region, eg --rescale 251 > > > > > > Thanks, > > > Pradeep > > > > > > On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve > > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > > > > If you want to use partial volume correction, then you are > > better off > > > using mri_gtmpvc with the bbr registration, something like > > > > > > 1. To start, run > > > > > > gtmseg --s subject > > > > > > This will take a couple of hours and produces some > files needed > > > for GTM > > > PVC (which is used for GTM, MG, RBV). > > > > > > 2. You'd then register the PET to the anatomical with > bbregister > > > (probably with --t2 weighting). Make sure to save the > output > > as an LTA > > > (--lta). I usually use the mean TAC as the input. You > can do > > this in > > > parallel with #1. > > > > > > 3. You'd then run mri_gtmpvc, something like > > > > > > mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 > .01 --seg > > > gtmseg.mgz > > > --reg reg.lta --default-seg-merge --o gtmpvc.output > > > > > > PSF is the point-spread FWHM of the scanner; reg.lta > is the > > > registration from #2. By default, this will scale by pons. > > The output > > > will be gtm.stats.dat and gtm.nii.gz. They both basically > > have the > > > same information. gtm.stats.dat is an easy to read text > > file. Where > > > each row is an ROI, something like: > > > > > > 9 17 Left-Hippocampus subcort_gm 473 > > > 174.083 1.406 0.1216 > > > > > > 9 = nineth row > > > 17 = index for RO > > > Left-Hippocampus = name of ROI > > > subcort_gm = tissue class > > > 473 = number of PET voxels in the ROI > > > 174 = variance reduction factor for ROI (based on > GLM/SGTM) > > > 1.406 = PVC uptake of ROI relative to Pons > > > 0.1216 = resdiual varaince across voxels in the ROI > > > > > > gtm.nii.gz is a nifti file with each "voxel" being an ROI. > > The value > > > is the PVC uptake of ROI relative to Pons. These can > easily be > > > concatenated together (mri_concat) and used as input to > > mri_glmfit > > > for group analysis. > > > > > > > > > > > > > > > On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > > > > Dear Freesurfer experts! > > > > > > > > I am currently working on PET analysis using FS > > > > > > > > I coregistered my PET with the processed MR using > bbregister, > > > > transfered it to a surface using mri_vol2surf > > > > and now createt an overlay in freeview with the > > lh.inflated and > > > used the > > > > labels from the lh.aparc.a2009s.annot file. > > > > > > > > In freeview i get the corresponding BP value for each > > vertex now but > > > > is there a way to get a list of vertices with the > > corresponding > > > BP value > > > > and the corresponding ROI this vertex belongs to? > > > > Or is there a better to do this analyis? > > > > > > > > Many thanks in advance! > > > > > > > > Benjamin > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://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> > > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://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> > > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto: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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> <mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Doug,
Thanks for your answer! I already tried this workflow but basically I am interested in a surface-based analysis. Is it possible by using this workflow to get the any stats.dat just for surface-ROIs?
Best, Benjamin Spurny
On Fr, 29.01.2016, 01:34, Douglas N Greve wrote:
On 01/28/2016 06:50 PM, Pradeep wrote:
Hello Doug,
I have used the gtmseg with --keep-cc flag and the corresponding ctab files showed the labels but the mri_gtmpvc step failed.
Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
What is your mri_gtmpvc command line? What is the rest of the terminal output?
My objective is to use the combination of all CC's as a reference region and obtain the PVC results, which would be listed in gtm.stats.dat
It will be best to combine them when running mri_gtmpvc using --replace, eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 this will cause all segments of the CC to appear to be a single segment (251).
Also, I read in the previous email discussions that the default ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with another ROI as a reference region, would it be OK take a ratio of the ROI's in gtm.stats.dat table.
Yes, or you can spec the new region, eg --rescale 251
Thanks, Pradeep
On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you want to use partial volume correction, then you are betteroff using mri_gtmpvc with the bbr registration, something like
1. To start, run gtmseg --s subject This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV). 2. You'd then register the PET to the anatomical with bbregister (probably with --t2 weighting). Make sure to save the output as anLTA (--lta). I usually use the mean TAC as the input. You can do this in parallel with #1.
3. You'd then run mri_gtmpvc, something like mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg gtmseg.mgz --reg reg.lta --default-seg-merge --o gtmpvc.output PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. By default, this will scale by pons. Theoutput will be gtm.stats.dat and gtm.nii.gz. They both basically have the same information. gtm.stats.dat is an easy to read text file. Where each row is an ROI, something like:
9 17 Left-Hippocampus subcort_gm 473 174.083 1.406 0.1216 9 = nineth row 17 = index for RO Left-Hippocampus = name of ROI subcort_gm = tissue class 473 = number of PET voxels in the ROI 174 = variance reduction factor for ROI (based on GLM/SGTM) 1.406 = PVC uptake of ROI relative to Pons 0.1216 = resdiual varaince across voxels in the ROI gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value is the PVC uptake of ROI relative to Pons. These can easily be concatenated together (mri_concat) and used as input to mri_glmfit for group analysis. On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > Dear Freesurfer experts! > > I am currently working on PET analysis using FS > > I coregistered my PET with the processed MR using bbregister, > transfered it to a surface using mri_vol2surf > and now createt an overlay in freeview with the lh.inflated and used the > labels from the lh.aparc.a2009s.annot file. > > In freeview i get the corresponding BP value for each vertex nowbut > is there a way to get a list of vertices with the corresponding BP value > and the corresponding ROI this vertex belongs to? > Or is there a better to do this analyis? > > Many thanks in advance! > > Benjamin > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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.edumailto: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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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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Hi Benjamin, do you still have a question about this? I lost the thread so please summarize the problem again. thanks doug
On 02/09/2016 05:01 AM, Benjamin Spurny wrote:
Hello Doug,
Thanks for your answer! I already tried this workflow but basically I am interested in a surface-based analysis. Is it possible by using this workflow to get the any stats.dat just for surface-ROIs?
Best, Benjamin Spurny
On Fr, 29.01.2016, 01:34, Douglas N Greve wrote:
On 01/28/2016 06:50 PM, Pradeep wrote:
Hello Doug,
I have used the gtmseg with --keep-cc flag and the corresponding ctab files showed the labels but the mri_gtmpvc step failed.
Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
What is your mri_gtmpvc command line? What is the rest of the terminal output?
My objective is to use the combination of all CC's as a reference region and obtain the PVC results, which would be listed in gtm.stats.dat
It will be best to combine them when running mri_gtmpvc using --replace, eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 this will cause all segments of the CC to appear to be a single segment (251).
Also, I read in the previous email discussions that the default ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with another ROI as a reference region, would it be OK take a ratio of the ROI's in gtm.stats.dat table.
Yes, or you can spec the new region, eg --rescale 251
Thanks, Pradeep
On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you want to use partial volume correction, then you are betteroff using mri_gtmpvc with the bbr registration, something like
1. To start, run gtmseg --s subject This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV). 2. You'd then register the PET to the anatomical with bbregister (probably with --t2 weighting). Make sure to save the output as anLTA (--lta). I usually use the mean TAC as the input. You can do this in parallel with #1.
3. You'd then run mri_gtmpvc, something like mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg gtmseg.mgz --reg reg.lta --default-seg-merge --o gtmpvc.output PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. By default, this will scale by pons. Theoutput will be gtm.stats.dat and gtm.nii.gz. They both basically have the same information. gtm.stats.dat is an easy to read text file. Where each row is an ROI, something like:
9 17 Left-Hippocampus subcort_gm 473 174.083 1.406 0.1216 9 = nineth row 17 = index for RO Left-Hippocampus = name of ROI subcort_gm = tissue class 473 = number of PET voxels in the ROI 174 = variance reduction factor for ROI (based on GLM/SGTM) 1.406 = PVC uptake of ROI relative to Pons 0.1216 = resdiual varaince across voxels in the ROI gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value is the PVC uptake of ROI relative to Pons. These can easily be concatenated together (mri_concat) and used as input to mri_glmfit for group analysis. On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > Dear Freesurfer experts! > > I am currently working on PET analysis using FS > > I coregistered my PET with the processed MR using bbregister, > transfered it to a surface using mri_vol2surf > and now createt an overlay in freeview with the lh.inflated and used the > labels from the lh.aparc.a2009s.annot file. > > In freeview i get the corresponding BP value for each vertex nowbut > is there a way to get a list of vertices with the corresponding BP value > and the corresponding ROI this vertex belongs to? > Or is there a better to do this analyis? > > Many thanks in advance! > > Benjamin > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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.edumailto: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.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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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Hi Doug,
Yes kind of, I am just looking for a way to read out PET data from a surface. I want to do an ROI-based analysis just on brainsurfaces of PET data.
What I did so far is that I coregistered the PET with the MR and used to vol2surf function to project my surface on the fsaverage with each subject.
Is there now a method to read the .mgh files of the surfaces ROI-based using the Desikan atlas?
Currently I am reading them out in Matlab using the .mgh file of my subjects surface and the .annot file from the fsaverage. I just wondered if there is a way to do this in Freesurfer as well?
Best, Benjamin
Am 16.02.2016 20:56, schrieb Douglas N Greve:
Hi Benjamin, do you still have a question about this? I lost the thread so please summarize the problem again. thanks doug
On 02/09/2016 05:01 AM, Benjamin Spurny wrote:
Hello Doug,
Thanks for your answer! I already tried this workflow but basically I am interested in a surface-based analysis. Is it possible by using this workflow to get the any stats.dat just for surface-ROIs?
Best, Benjamin Spurny
On Fr, 29.01.2016, 01:34, Douglas N Greve wrote:
On 01/28/2016 06:50 PM, Pradeep wrote:
Hello Doug,
I have used the gtmseg with --keep-cc flag and the corresponding ctab files showed the labels but the mri_gtmpvc step failed.
Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
What is your mri_gtmpvc command line? What is the rest of the terminal output?
My objective is to use the combination of all CC's as a reference region and obtain the PVC results, which would be listed in gtm.stats.dat
It will be best to combine them when running mri_gtmpvc using --replace, eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 this will cause all segments of the CC to appear to be a single segment (251).
Also, I read in the previous email discussions that the default ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with another ROI as a reference region, would it be OK take a ratio of the ROI's in gtm.stats.dat table.
Yes, or you can spec the new region, eg --rescale 251
Thanks, Pradeep
On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you want to use partial volume correction, then you arebetter off using mri_gtmpvc with the bbr registration, something like
1. To start, run gtmseg --s subject This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV). 2. You'd then register the PET to the anatomical withbbregister (probably with --t2 weighting). Make sure to save the output as an LTA (--lta). I usually use the mean TAC as the input. You can do this in parallel with #1.
3. You'd then run mri_gtmpvc, something like mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01--seg gtmseg.mgz --reg reg.lta --default-seg-merge --o gtmpvc.output
PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. By default, this will scale by pons. Theoutput will be gtm.stats.dat and gtm.nii.gz. They both basically have the same information. gtm.stats.dat is an easy to read text file. Where each row is an ROI, something like:
9 17 Left-Hippocampus subcort_gm 473 174.083 1.406 0.1216 9 = nineth row 17 = index for RO Left-Hippocampus = name of ROI subcort_gm = tissue class 473 = number of PET voxels in the ROI 174 = variance reduction factor for ROI (based on GLM/SGTM) 1.406 = PVC uptake of ROI relative to Pons 0.1216 = resdiual varaince across voxels in the ROI gtm.nii.gz is a nifti file with each "voxel" being an ROI. Thevalue is the PVC uptake of ROI relative to Pons. These can easily be concatenated together (mri_concat) and used as input to mri_glmfit for group analysis.
On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > Dear Freesurfer experts! > > I am currently working on PET analysis using FS > > I coregistered my PET with the processed MR using bbregister, > transfered it to a surface using mri_vol2surf > and now createt an overlay in freeview with the lh.inflatedand used the > labels from the lh.aparc.a2009s.annot file. > > In freeview i get the corresponding BP value for each vertex now but > is there a way to get a list of vertices with the corresponding BP value > and the corresponding ROI this vertex belongs to? > Or is there a better to do this analyis? > > Many thanks in advance! > > Benjamin > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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.edumailto: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 personto 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
If you are not doing PVC, then the easiest (and most accurate) will be to map the PET to the individual anatomical space, then use mri_segstats with aparc+aseg.mgz as the segmentation to compute the mean in each ROI. If you want to continue with your stream, you can use mri_segstats using --annot fsaverage lh aparc
On 02/17/2016 09:26 AM, Benjamin Spurny wrote:
Hi Doug,
Yes kind of, I am just looking for a way to read out PET data from a surface. I want to do an ROI-based analysis just on brainsurfaces of PET data.
What I did so far is that I coregistered the PET with the MR and used to vol2surf function to project my surface on the fsaverage with each subject.
Is there now a method to read the .mgh files of the surfaces ROI-based using the Desikan atlas?
Currently I am reading them out in Matlab using the .mgh file of my subjects surface and the .annot file from the fsaverage. I just wondered if there is a way to do this in Freesurfer as well?
Best, Benjamin
Am 16.02.2016 20:56, schrieb Douglas N Greve:
Hi Benjamin, do you still have a question about this? I lost the thread so please summarize the problem again. thanks doug
On 02/09/2016 05:01 AM, Benjamin Spurny wrote:
Hello Doug,
Thanks for your answer! I already tried this workflow but basically I am interested in a surface-based analysis. Is it possible by using this workflow to get the any stats.dat just for surface-ROIs?
Best, Benjamin Spurny
On Fr, 29.01.2016, 01:34, Douglas N Greve wrote:
On 01/28/2016 06:50 PM, Pradeep wrote:
Hello Doug,
I have used the gtmseg with --keep-cc flag and the corresponding ctab files showed the labels but the mri_gtmpvc step failed.
Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
What is your mri_gtmpvc command line? What is the rest of the terminal output?
My objective is to use the combination of all CC's as a reference region and obtain the PVC results, which would be listed in gtm.stats.dat
It will be best to combine them when running mri_gtmpvc using --replace, eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 this will cause all segments of the CC to appear to be a single segment (251).
Also, I read in the previous email discussions that the default ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with another ROI as a reference region, would it be OK take a ratio of the ROI's in gtm.stats.dat table.
Yes, or you can spec the new region, eg --rescale 251
Thanks, Pradeep
On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you want to use partial volume correction, then you arebetter off using mri_gtmpvc with the bbr registration, something like
1. To start, run gtmseg --s subject This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV). 2. You'd then register the PET to the anatomical withbbregister (probably with --t2 weighting). Make sure to save the output as an LTA (--lta). I usually use the mean TAC as the input. You can do this in parallel with #1.
3. You'd then run mri_gtmpvc, something like mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01--seg gtmseg.mgz --reg reg.lta --default-seg-merge --o gtmpvc.output
PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. By default, this will scale by pons. Theoutput will be gtm.stats.dat and gtm.nii.gz. They both basically have the same information. gtm.stats.dat is an easy to read text file. Where each row is an ROI, something like:
9 17 Left-Hippocampus subcort_gm 473 174.083 1.406 0.1216 9 = nineth row 17 = index for RO Left-Hippocampus = name of ROI subcort_gm = tissue class 473 = number of PET voxels in the ROI 174 = variance reduction factor for ROI (based on GLM/SGTM) 1.406 = PVC uptake of ROI relative to Pons 0.1216 = resdiual varaince across voxels in the ROI gtm.nii.gz is a nifti file with each "voxel" being an ROI. Thevalue is the PVC uptake of ROI relative to Pons. These can easily be concatenated together (mri_concat) and used as input to mri_glmfit for group analysis.
On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > Dear Freesurfer experts! > > I am currently working on PET analysis using FS > > I coregistered my PET with the processed MR using bbregister, > transfered it to a surface using mri_vol2surf > and now createt an overlay in freeview with the lh.inflatedand used the > labels from the lh.aparc.a2009s.annot file. > > In freeview i get the corresponding BP value for each vertex now but > is there a way to get a list of vertices with the corresponding BP value > and the corresponding ROI this vertex belongs to? > Or is there a better to do this analyis? > > Many thanks in advance! > > Benjamin > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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.edumailto: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 personto 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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@nmr.mgh.harvard.edu