Try using --replace 29 2
On 12/29/2020 12:48 PM, Julie Ottoy wrote:
External Email - Use Caution
Hi Doug
Thanks for your reply. I tried both your suggestions, but it seems as though
they both ran into an error.
For your first suggestion, i.e. adding --replace 29 3 to the command line of
gtmpvc, I get the error:
Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz
Loading seg ctab 057_S_5295re/mri/gtmseg.ctab
Reading 057_S_5295re/mri/gtmseg.lta
Replacing 19
Pruning ctab
ERROR: CTABpruneCTab(): ctab does not have segid 3
For your second suggestion, i.e. I replaced the following line in the ctab:
29 Left-undetermined 135 206 235 0 -1
==> replaced by: 29 Left-undetermined 135 206 235 0 3
I get the error:
Computing Seg in input space
Building GTM DoVoxFracCor=0
ERROR: creating region for nthseg=12, segid=29, Left-undetermined
It may be that there are no voxels for this seg when mapped into the input
space.
Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the
registration
Build time 5.9690, err = 1
Thank you,
Julie
On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
You can use the fix from my previous email or you can add the following line
any were into the gtmseg.ctab file:
29 Left-undetermined 135 206 235 0 3
On 12/18/2020 11:06 PM, Julie Ottoy wrote:
External Email - Use Caution
Sorry I would like to correct my previous post. The subject also failed with
PVC.
I see now that the issue is happening during the gtm seg stage where it gives
the error: WARNING: segid 29 Left-undetermined tissue type is not set.
For your information: I ran the standard FS and petsurfer pipeline as outlined
on the wiki. I tried two gtm seg commands:
gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
Thank you for your help,
Julie
On Fri, 18 Dec 2020 at 00:09, Julie Ottoy
<julie.jj.ot...@gmail.com<mailto:julie.jj.ot...@gmail.com>> wrote:
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Dear Doug,
I have the same issue as the people below. I was wondering if this was solved
in the meantime.
I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and got
the following error in only one of my subjects. When I ran the same subject
with PVC and specified psf, it did run fine.
$Id: mri_gtmpvc.c,-
setenv -
cd -
mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg gtmseg.mgz
--default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o
/gtmnopvc.output.ceregrey --rescale 8 47
sysname Linux
hostname -
machine -
user -
vgthresh 0.001000
nReplace 18
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
24 avail.processors, using 1
Creating output directory /gtmnopvc.output.ceregrey
Loading seg for gtm /ID/mri/gtmseg.mgz
Loading seg ctab /ID/mri/gtmseg.ctab
Reading /ID/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set
Failed tissue type check
Any suggestions would be appreciated!
Thank you,
Julie
Re: [Freesurfer] mri_gtmpvc error: failed tissue type
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Douglas
Greve<https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV4jNz4fwyUMZPIMoCVdt9d_bUFEK6r8QndJ4GnxUzSJ5nFbTzLdgAE-xzB-cDHXFlDfjsbfBplG7gX0td56lZUCF6RZPQS86X8fx38fzgpoQ3ODino_OhrbrTLu_vxfi-hx0Kk2lh3HyNlKDTzyXnTgdkp2Aal7nkVZSeRuXTLXG3JF5hoKLtnmjEillAunhi3_Opx8m7CSxBHkkUEndRqMO7hLRg4xySjrREex2pQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BGreve%2522%26o%3Dnewest%26f%3D1>
sorry, can you send me the details again?
On 11/21/17 10:24 AM, Klein, Gregory wrote:
Hello Donatas and Douglas,
Did you ever find a cause and solution for this problem? I too
occasionally get this error message, and cannot get the results of
mri_gtmpvc for certain subjects.
Any suggestions are welcome.
Thanks,
Greg
--
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Bldg 01, Floor 16, N445
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Re: [Freesurfer] mri_gtmpvc error: failed tissue type
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Douglas N
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Donatas, please remember to include previous correspondence so that we
have everything in one email. Can you upload your freesurfer subject so
that I can debug it further? upload to
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On 11/09/2016 12:17 PM, Donatas Sederevicius wrote:
>
> I followed the processing workflow as described in PETSurfer wiki
> and gtmseg.mgz was created using gtmseg script as described. I
> ran this processing for over 100 subjects and only one has failed.
>
>
>
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Re: [Freesurfer] mri_gtmpvc error: failed tissue type
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Donatas
Sederevicius<https://secure-web.cisco.com/1JNZMWhSBxxqZ4whfRrQXZBTWg88CVAVN7kKCidcLVIRKlwU3UP25xnszjeeOUSTu4MAOtS07GmVt_x7VvtqpQoEAaS71PvpUOuuh2Jakccv8UApdQNTlnQdUnmjNnHmlGvLcg5IUijE2zaZXa9RYA8IDK_ah32UsYDVwGsJEoTOmWJw7z4syagjpNSb-3Md12zplk8Bk_VyLPOioLaFuLwkId-HkmUwYihnJP3FHPaoBvcC9nZcNp9aLf_oWZSt-7iToV4Zqf-IpHtddQTUy0A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Donatas%2BSederevicius%2522%26o%3Dnewest%26f%3D1>
I followed the processing workflow as described in PETSurfer wiki and
gtmseg.mgz was created using gtmseg script as described. I ran this processing
for over 100 subjects and only one has failed.
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Re: [Freesurfer] mri_gtmpvc error: failed tissue type
check<https://secure-web.cisco.com/1vPxlf-9EcToYjQ2NcohNFPvheryGJhjZq4nxdkmbOKRg2omA5NkvMb0IblIRORZ1EoUy_uNZK78n0cJGkdzgNLgkKgbgrH6CwMUbGRrwurpX7PEF7YXvBsk3iQvBzt9B4WWXE2dF2qCPythWj_9RDNWO3rOCKW7J8-CFgKSLi4xVEHJtYnueAy-zQquTDSQGbXCyL47s3SpPzQZ6RX88M2Qf0zVigwKGWTeW9-6AOasIs7vnUUsbSasf1jSg1sKh9CeEzsLQstjOfhvzBEhNEg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg50018.html>
2016-11-09<https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkAZk8D_towDhzokqKY_qAQwhvC1t3LAMD69EKL6P5LScJWmhzwCjRBuSg7VzqL6g83C8d5pyJjtz5eqtsIlEQN85STIBFvGtUVLKU2XG0l5kr78h30dIzDum_UKXAyP_jpbOnx_VKSbmtieMeOYTumJYcyCcdTfrnLSUO4WN-kp10g8XORxRwDJZA_c02mHkmmEuJCXGaPsflUoQJRc3evAQquLrXiu8gGFbfE5ayEQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Ddate%3A20161109%26o%3Dnewest%26f%3D1>
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Douglas
Greve<https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV4jNz4fwyUMZPIMoCVdt9d_bUFEK6r8QndJ4GnxUzSJ5nFbTzLdgAE-xzB-cDHXFlDfjsbfBplG7gX0td56lZUCF6RZPQS86X8fx38fzgpoQ3ODino_OhrbrTLu_vxfi-hx0Kk2lh3HyNlKDTzyXnTgdkp2Aal7nkVZSeRuXTLXG3JF5hoKLtnmjEillAunhi3_Opx8m7CSxBHkkUEndRqMO7hLRg4xySjrREex2pQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BGreve%2522%26o%3Dnewest%26f%3D1>
Was gtmseg.mgz created with the gtmseg script?
On 11/9/16 4:43 AM, Donatas Sederevicius wrote:
Dear Freesurfer community,
An error has occured while applying PET partial volume correction
using mri_gtmpvc. A snippet from the log file:
Reading /projects/PET/recon/ID247/mri/gtmseg.lta
Replacing 18
ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined
not set
Failed tissue type check
gtmseg was run as: gtmseg --s ID247 and completed without errors.
mri_gtmpvc was run as:
mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz
--psf 2 --no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz
--reg /projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge
--o /projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled
--save-input --km-ref 8 47 --km-hb 11 12 13 50 51 52
How could this problem be solved?
Thank you.
Best regards,
Donatas
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[Freesurfer] mri_gtmpvc error: failed tissue type
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2016-11-09<https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkAZk8D_towDhzokqKY_qAQwhvC1t3LAMD69EKL6P5LScJWmhzwCjRBuSg7VzqL6g83C8d5pyJjtz5eqtsIlEQN85STIBFvGtUVLKU2XG0l5kr78h30dIzDum_UKXAyP_jpbOnx_VKSbmtieMeOYTumJYcyCcdTfrnLSUO4WN-kp10g8XORxRwDJZA_c02mHkmmEuJCXGaPsflUoQJRc3evAQquLrXiu8gGFbfE5ayEQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Ddate%3A20161109%26o%3Dnewest%26f%3D1>
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Donatas
Sederevicius<https://secure-web.cisco.com/1JNZMWhSBxxqZ4whfRrQXZBTWg88CVAVN7kKCidcLVIRKlwU3UP25xnszjeeOUSTu4MAOtS07GmVt_x7VvtqpQoEAaS71PvpUOuuh2Jakccv8UApdQNTlnQdUnmjNnHmlGvLcg5IUijE2zaZXa9RYA8IDK_ah32UsYDVwGsJEoTOmWJw7z4syagjpNSb-3Md12zplk8Bk_VyLPOioLaFuLwkId-HkmUwYihnJP3FHPaoBvcC9nZcNp9aLf_oWZSt-7iToV4Zqf-IpHtddQTUy0A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Donatas%2BSederevicius%2522%26o%3Dnewest%26f%3D1>
Dear Freesurfer community,
An error has occured while applying PET partial volume correction using
mri_gtmpvc. A snippet from the log file:
Reading /projects/PET/recon/ID247/mri/gtmseg.lta
Replacing 18
ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set
Failed tissue type check
gtmseg was run as: gtmseg --s ID247 and completed without errors.
mri_gtmpvc was run as:
mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz --psf 2
--no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz --reg
/projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge --o
/projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled --save-input
--km-ref 8 47 --km-hb 11 12 13 50 51 52
How could this problem be solved?
Thank you.
Best regards,
Donatas
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