Hello,
Is there a way to save the PVC (RBV) output in native PET resolution, before upsampling?
Would you also be able to share the command that is used for upsampling? I would like to play with a different type of interpolation.
Thank you very much.
Su
It is not set up to do it this way, but there is a work-around. Run mri_gtmpvc without --rbv but with --no-reduce-fov, then run it again specifying the gtmpvcoutput/seg/seg.nii.gz file as the segmentation and --regheader instead of --reg.
On 12/05/2016 11:52 AM, SudEEpti wrote:
Hello,
Is there a way to save the PVC (RBV) output in native PET resolution, before upsampling?
Would you also be able to share the command that is used for upsampling? I would like to play with a different type of interpolation.
Thank you very much.
Su
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I tried the following, but the program seems to seg fault. No output files are created. Please let me know what you think I might be missing. Thank you!
mri_gtmpvc --i pet.nii.gz --seg gtmseg.mgz --reg reg.lta --o $PWD/s1
--no-reduce-fov
*mri_gtmpvc done*
mri_gtmpvc --i pet.nii.gz --seg $PWD/s1/aux/seg.nii.gz --regheader --o
$PWD/s2 --rbv *Segmentation fault (core dumped)*
On Mon, Dec 5, 2016 at 5:21 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
It is not set up to do it this way, but there is a work-around. Run mri_gtmpvc without --rbv but with --no-reduce-fov, then run it again specifying the gtmpvcoutput/seg/seg.nii.gz file as the segmentation and --regheader instead of --reg.
On 12/05/2016 11:52 AM, SudEEpti wrote:
Hello,
Is there a way to save the PVC (RBV) output in native PET resolution, before upsampling?
Would you also be able to share the command that is used for upsampling? I would like to play with a different type of interpolation.
Thank you very much.
Su
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.
Can you send the full terminal output?
On 6/27/17 4:15 PM, SudEEpti wrote:
I tried the following, but the program seems to seg fault. No output files are created. Please let me know what you think I might be missing. Thank you!
mri_gtmpvc --i pet.nii.gz --seg gtmseg.mgz --reg reg.lta --o $PWD/s1
--no-reduce-fov /mri_gtmpvc done /
mri_gtmpvc --i pet.nii.gz --seg $PWD/s1/aux/seg.nii.gz --regheader
--o $PWD/s2 --rbv /Segmentation fault (core dumped)/
On Mon, Dec 5, 2016 at 5:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is not set up to do it this way, but there is a work-around. Run mri_gtmpvc without --rbv but with --no-reduce-fov, then run it again specifying the gtmpvcoutput/seg/seg.nii.gz file as the segmentation and --regheader instead of --reg. On 12/05/2016 11:52 AM, SudEEpti wrote: > Hello, > > Is there a way to save the PVC (RBV) output in native PET resolution, > before upsampling? > > Would you also be able to share the command that is used for > upsampling? I would like to play with a different type of interpolation. > > Thank you very much. > > Su > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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/ <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 <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 <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
I tried the following, but the program seems to seg fault. No output files are created. Please help! Thank you.
Alternatively, is there a way to generate the "nopvc" image in RBV space? Thanks!
*>>mri_gtmpvc --i pet.nii.gz --reg pet2mri.lta --psf 6 --seg gtmseg.mgz --no-reduce-fov --o pvcout*
sysname Linux
hostname rair-pipeline.avidrp.com
machine x86_64
user imagingsciences
vgthresh 0.001000
nReplace 0
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
12 avail.processors, using 1
Creating output directory pvcout
Loading seg for gtm gtmseg.mgz
Loading seg ctab gtmseg.ctab
Reading gtmseg.lta
Pruning ctab
done with seg vol
maxFWHM = 3 (voxels), PadThresh=0.0001, nPad=10
Data load time 21.4 sec
nmask = 770048, nsegs = 111, excluding segid=0
FWHM: 6 6 6
Std: 2.54797 2.54797 2.54797
nPad 10, PadThresh 0.0001
Checking Ref Ids
Segmentations used for rescaling
174 Pons
Computing Seg PVF
MRIseg2SegPVF(): Initilizing cache nsegs = 111, nvox = 770048, nthreads=1, DoSeg=0
resmm=0.5 c: 2 4 -0.375 0.25, r: 2 4 -0.375 0.25, s: 3.27 7 -0.428571 0.142857
delta 0.5 0.5 0.467143, npervox = 112
MRIseg2SegPVF(): done t = 3.651, nhits=30403821, nthreads=1
Computing Seg in input space
Building GTM DoVoxFracCor=1
Build time 7.9280, err = 0
gtm build time 7.9 sec
Solving ...
Computing XtX ... 86.2 sec
gtm multiplicative scale 0.00133486
Time to solve 88.2 sec
Writing seg vrf to pvcout/aux/seg.vrf.nii.gz
Writing seg nvox to pvcout/aux/seg.nvox.nii.gz
Computing global stats
Global S: 70911.734375 114222.078125 129324.281250
Global N: 45702 86756 128678
Computing percent TT in each ROI
Writing tt percent to pvcout/aux/seg.ttpct.nii.gz
Freeing X
rescale factor 0.001334858730981
Writing GTM beta estimates to pvcout/gtm.nii.gz
Writing var of GTM estimates to pvcout/gtm.var.nii.gz
rvar = 0.0300172
XtX Condition 1453366.625
Freeing X0
rvargm 0 0.0186
XtX Condition 1453366.625
VRF Mean/Min/Max 1118.000 0.042 51245.551
Writing seg rvar estimates to pvcout/aux/seg.rvar.nii.gz
Freeing y
MEM: Size 1400528 Peak: 2080860 RSS: 604616 Data: 1263208 Stk: 92
mri_gtmpvc-runtime 2.46 min
mri_gtmpvc done
*>>mri_gtmpvc --i pet.nii.gz --psf 6 --seg pvcout/aux/seg.nii.gz --regheader --rbv --debug*
Segmentation fault (core dumped)
On Mon, Dec 5, 2016 at 5:21 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
It is not set up to do it this way, but there is a work-around. Run mri_gtmpvc without --rbv but with --no-reduce-fov, then run it again specifying the gtmpvcoutput/seg/seg.nii.gz file as the segmentation and --regheader instead of --reg.
On 12/05/2016 11:52 AM, SudEEpti wrote:
Hello,
Is there a way to save the PVC (RBV) output in native PET resolution, before upsampling?
Would you also be able to share the command that is used for upsampling? I would like to play with a different type of interpolation.
Thank you very much.
Su
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.
After some investigation, I found that that command will not work. You can run it in the normal way, and then run
mri_vol2vol --mov rbv.nii.gz --targ pet.nii.gz --regheader --fill-average
This will average all the rbv voxels that fall into a pet voxel (or you could use --interp nearest|trilin|cubic)
On 07/18/2017 12:34 PM, SudEEpti wrote:
I tried the following, but the program seems to seg fault. No output files are created. Please help! Thank you.
Alternatively, is there a way to generate the "nopvc" image in RBV space? Thanks!
*>>mri_gtmpvc --i pet.nii.gz --reg pet2mri.lta --psf 6 --seg gtmseg.mgz --no-reduce-fov --o pvcout*
sysnameLinux
hostname rair-pipeline.avidrp.com http://rair-pipeline.avidrp.com
machinex86_64
user imagingsciences
vgthresh 0.001000
nReplace 0
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
12 avail.processors, using 1
Creating output directory pvcout
Loading seg for gtm gtmseg.mgz
Loading seg ctab gtmseg.ctab
Reading gtmseg.lta
Pruning ctab
done with seg vol
maxFWHM = 3 (voxels), PadThresh=0.0001, nPad=10
Data load time 21.4 sec
nmask = 770048, nsegs = 111, excluding segid=0
FWHM: 6 6 6
Std:2.54797 2.54797 2.54797
nPad 10, PadThresh 0.0001
Checking Ref Ids
Segmentations used for rescaling
174 Pons
Computing Seg PVF
MRIseg2SegPVF(): Initilizing cache nsegs = 111, nvox = 770048, nthreads=1, DoSeg=0
resmm=0.5 c: 2 4 -0.375 0.25, r: 2 4 -0.375 0.25, s: 3.27 7 -0.428571 0.142857
delta 0.5 0.5 0.467143, npervox = 112
MRIseg2SegPVF(): done t = 3.651, nhits=30403821, nthreads=1
Computing Seg in input space
Building GTM DoVoxFracCor=1
Build time 7.9280, err = 0
gtm build time7.9 sec
Solving ...
ComputingXtX ...86.2 sec
gtm multiplicative scale 0.00133486
Time to solve 88.2 sec
Writing seg vrf to pvcout/aux/seg.vrf.nii.gz
Writing seg nvox to pvcout/aux/seg.nvox.nii.gz
Computing global stats
Global S: 70911.734375 114222.078125 129324.281250
Global N: 45702 86756 128678
Computing percent TT in each ROI
Writing tt percent to pvcout/aux/seg.ttpct.nii.gz
Freeing X
rescale factor0.001334858730981
Writing GTM beta estimates to pvcout/gtm.nii.gz
Writing var of GTM estimates to pvcout/gtm.var.nii.gz
rvar = 0.0300172
XtXCondition 1453366.625
Freeing X0
rvargm0 0.0186
XtXCondition 1453366.625
VRFMean/Min/Max1118.0000.042 51245.551
Writing seg rvar estimates to pvcout/aux/seg.rvar.nii.gz
Freeing y
MEM: Size 1400528Peak: 2080860 RSS: 604616Data: 1263208Stk: 92
mri_gtmpvc-runtime2.46 min
mri_gtmpvc done
*>>mri_gtmpvc --i pet.nii.gz --psf 6 --seg pvcout/aux/seg.nii.gz --regheader --rbv --debug*
Segmentation fault (core dumped)
On Mon, Dec 5, 2016 at 5:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is not set up to do it this way, but there is a work-around. Run mri_gtmpvc without --rbv but with --no-reduce-fov, then run it again specifying the gtmpvcoutput/seg/seg.nii.gz file as the segmentation and --regheader instead of --reg. On 12/05/2016 11:52 AM, SudEEpti wrote: > Hello, > > Is there a way to save the PVC (RBV) output in native PET resolution, > before upsampling? > > Would you also be able to share the command that is used for > upsampling? I would like to play with a different type of interpolation. > > Thank you very much. > > Su > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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/ <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 <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 <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
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
SudEEpti