Re: [Freesurfer] Reading values from overlays with PETcoreg

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>
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    <mailto:greve@nmr.mgh.harvard.edu>>
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    <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
    >     >     >     >
    >     >     >     >
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    >     >
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    >     <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
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    >     >
    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/
    >
    >  _______________________________________________
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    --
    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/

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