Re: [Freesurfer] mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg

2021-04-06 Thread Bahar Hazal Yalçınkaya 
External Email - Use Caution

Thank you Douglas, I tried quickly via correcting my gtmseg.ctab output
with standardized for gtmseg only for tissue types, it runs without error,
I will create a new look up table and try further.

Thanks again,
Kind regards.

On Tue, Apr 6, 2021 at 3:53 PM Douglas N. Greve 
wrote:

> gtmseg will not give an error, but the color table that gtmseg outputs
> will not be right and needs to be fixed.
>
> On 4/6/2021 9:41 AM, Bahar Hazal Yalçınkaya wrote:
>
> External Email - Use Caution
> Thanks for response, color table and annotations are there "--ctx-annot
> Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab
> Schaefer2018_400Parcels_7Networks_order_LUT.txt", gtmseg did not gave an
> error, you can see at attachments. (Also I can see 258 Head segmentation in 
> *gtmseg.ctab
> *file) also mri_coreg is working well (see also attachments). The problem
> is the "*mri_gtmpvc*" command where it fails while checking tissue types
> more precisely it complains about Head segmentation.
>
> I run with standard options. I checked everything I can think of, each
> file and image seems to be similar but still could not find a proper
> solution. Is there anything specific I need to check?
> Thanks in advance,
> Kind regards
>
> On Tue, Apr 6, 2021 at 3:26 PM Douglas N. Greve 
> wrote:
>
>> You will need to create a new color table. This is not hard, but not easy
>> either. First, there should be a color table already there. I'm not sure
>> what that will be like; it might have your segments in it, it might not. It
>> might be easier to run gtmseg with the standard options and look at the
>> color table, then try to replicate it with your segmentation
>>
>> On 4/5/2021 6:43 AM, Bahar Hazal Yalçınkaya wrote:
>>
>> External Email - Use Caution
>> Hello Freesurfer"s Developers,
>>
>> I am trying to follow *PetSurfer* (*MailScanner has detected a possible
>> fraud attempt from "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1B2HO1KM0jnhlHMvubnOYbXX6eMhgWiZ6pFbmY8cJ2rCR2zh7VM-XMlmpKiWAzd5tpEcw6RAupdohvdRKmcJoaAgzRSY1dmGSjgmtdT6CARZGIoZpbZtWPP6y1VMM1fKmi4Psm_C57Invn3aAGEGE0zFpdyHGoW22HTxO2OCOQfY1hc_50vWrBdP468EQW9X5TzK4SepUR_s94d7KIzuv7hfNO_WUMrR3z8qtqTjb0jNNcQDGNKZ5HpdLi9nOSFrkv-V_F731T7DiDbbsXdd1Mw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer
>> )
>> to apply PVC to Pet images.
>> Default pipeline is working however, whenever i try to use another atlas,
>> Schaefer parcellation, mri_gtmpvc command I get following error:
>>
>> WARNING: LTAconcat(): inverting LTA 1 to match geometry
>>
>> Replacing 18
>>
>> Pruning ctab
>>
>> tissue type schema
>>
>> Checking tissue type
>>
>> ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral
>> not set
>>
>> Failed tissue type check
>>
>> I have searched to list several people who have issued similar errors but
>> unfortunately i could not find any solution that works for me. Below you
>> can find commands I used:
>>
>> $ gtmseg --s subject --o gtmseg.mgz --ctx-annot
>> Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab
>> Schaefer2018_400Parcels_7Networks_order_LUT.txt
>> $ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta
>> $ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta
>> --regheader --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx
>> .01 --km-ref 8 47 --o gtmpvc.output
>> Also I checked the run of gtmseg via "*tkmeditfv*" where i can visualise 258
>> Head-ExtraCerebral, and additionally I checked *gtmseg.ctab *file also 258
>> Head-ExtraCerebral in the list.
>> I will be happy to hear from you.
>> Kind regards.
>> --
>> Ph.D. Bahar Hazal Yalçınkaya
>>
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1bpF6vIi1TzZFN2hZ0kddt70_T6WpYlp2YZzHb5NmkZ84_1QPYWHPFG_xAVTFs0DyiO447A3zVtvA1ojS8Z8JosjVW8f3y0vj30YJkXv-aHu9fuTxZbXYw3yLNG_KcGHo4zuQVTUWWLdS1gC-8ruqQFYpqPr1xcicpcyTesO93J5fcSWFiwz4clzLYUFYIqTZloMS8RZXIBq8rdi8YpSJspibOvtmsyOKwwu0yTASPYGmgQhVxjSWyuVCfdVWPQ8xe0DtRPiILA2jkIQaxvO4aA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>>

Re: [Freesurfer] mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg

2021-04-06 Thread Douglas N. Greve 
gtmseg will not give an error, but the color table that gtmseg outputs 
will not be right and needs to be fixed.


On 4/6/2021 9:41 AM, Bahar Hazal Yalçınkaya wrote:


External Email - Use Caution

Thanks for response, color table and annotations are there 
"--ctx-annot Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 
--ctab Schaefer2018_400Parcels_7Networks_order_LUT.txt", gtmseg did 
not gave an error, you can see at attachments. (Also I can see 258 
Head segmentation in *gtmseg.ctab *file)also mri_coreg is working well 
(see also attachments). The problem is the "*mri_gtmpvc*" command 
where it fails while checking tissue types more precisely it complains 
about Head segmentation.


I run with standard options. I checked everything I can think of, each 
file and image seems to be similar but still could not find a proper 
solution. Is there anything specific I need to check?

Thanks in advance,
Kind regards

On Tue, Apr 6, 2021 at 3:26 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


You will need to create a new color table. This is not hard, but
not easy either. First, there should be a color table already
there. I'm not sure what that will be like; it might have your
segments in it, it might not. It might be easier to run gtmseg
with the standard options and look at the color table, then try to
replicate it with your segmentation

On 4/5/2021 6:43 AM, Bahar Hazal Yalçınkaya wrote:


External Email - Use Caution

Hello Freesurfer"s Developers,

I am trying to follow */PetSurfer/* (*MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to
be* https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer

)
to apply PVC to Pet images.
Default pipeline is working however, whenever i try to use
another atlas, Schaefer parcellation, mri_gtmpvc command I get
following error:
WARNING: LTAconcat(): inverting LTA 1 to match geometry

Replacing 18

Pruning ctab

tissue type schema

Checking tissue type

ERROR: CheckSegTissueType() tissue type for seg 258
Head-ExtraCerebral not set

Failed tissue type check


I have searched to list several people who have issued similar
errors but unfortunately i could not find any solution that works
for me. Below you can find commands I used:

$ gtmseg --s subject--o gtmseg.mgz
--ctx-annotSchaefer2018_400Parcels_7Networks_order.annot 1000
2000 --ctab Schaefer2018_400Parcels_7Networks_order_LUT.txt
$ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta
$ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta
--regheader --seg gtmseg.mgz --default-seg-merge --auto-mask PSF
.01 --mgx .01 --km-ref 8 47 --o gtmpvc.output
Also I checked the run of gtmseg via "*tkmeditfv*" where i can
visualise 258 Head-ExtraCerebral, and additionally I checked
*gtmseg.ctab *file also 258 Head-ExtraCerebral in the list.
I will be happy to hear from you.
Kind regards.
-- 
Ph.D. Bahar Hazal Yalçınkaya



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--
Ph.D. Bahar Hazal Yalçınkaya


___
Freesurf

Re: [Freesurfer] mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg

2021-04-06 Thread Douglas N. Greve 
You will need to create a new color table. This is not hard, but not 
easy either. First, there should be a color table already there. I'm not 
sure what that will be like; it might have your segments in it, it might 
not. It might be easier to run gtmseg with the standard options and look 
at the color table, then try to replicate it with your segmentation


On 4/5/2021 6:43 AM, Bahar Hazal Yalçınkaya wrote:


External Email - Use Caution

Hello Freesurfer"s Developers,

I am trying to follow */PetSurfer/* (*MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer 
) 
to apply PVC to Pet images.
Default pipeline is working however, whenever i try to use another 
atlas, Schaefer parcellation, mri_gtmpvc command I get following error:

WARNING: LTAconcat(): inverting LTA 1 to match geometry

Replacing 18

Pruning ctab

tissue type schema

Checking tissue type

ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral 
not set


Failed tissue type check


I have searched to list several people who have issued similar errors 
but unfortunately i could not find any solution that works for me. 
Below you can find commands I used:


$ gtmseg --s subject--o gtmseg.mgz 
--ctx-annotSchaefer2018_400Parcels_7Networks_order.annot 1000 2000 
--ctab Schaefer2018_400Parcels_7Networks_order_LUT.txt

$ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta
$ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta 
--regheader --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 
--mgx .01 --km-ref 8 47 --o gtmpvc.output
Also I checked the run of gtmseg via "*tkmeditfv*" where i can 
visualise 258 Head-ExtraCerebral, and additionally I checked 
*gtmseg.ctab *file also 258 Head-ExtraCerebral in the list.

I will be happy to hear from you.
Kind regards.
--
Ph.D. Bahar Hazal Yalçınkaya


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[Freesurfer] mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg

2021-04-05 Thread Bahar Hazal Yalçınkaya 
External Email - Use Caution

Hello Freesurfer"s Developers,

I am trying to follow *PetSurfer* (
https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwSGz7RCQalhqGZJFfIT2Ob3QQETtldwxv9y8xYVYGSkRdQ_GjplqWAGkIFRP1S40sf8UfJTbg-jdroEwAQvGW-9HmP1fatTZ8h3DhbPvM4MaRIdn-gicol4f85-JI5PjVoycwQ5z0q2oYvFmz9DuRwGJZg7EiKqmfCLYhXNUOPOwhpm1kKKikeaQrRAVCr4-WbYz4Z0GXBVuflZqXa84PEzxVj0uL51CZ_xoDuhu3DA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer)
 to apply PVC to Pet
images.
Default pipeline is working however, whenever i try to use another atlas,
Schaefer parcellation, mri_gtmpvc command I get following error:

WARNING: LTAconcat(): inverting LTA 1 to match geometry

Replacing 18

Pruning ctab

tissue type schema

Checking tissue type

ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral not
set

Failed tissue type check

I have searched to list several people who have issued similar errors but
unfortunately i could not find any solution that works for me. Below you
can find commands I used:

$ gtmseg --s subject --o gtmseg.mgz --ctx-annot
Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab
Schaefer2018_400Parcels_7Networks_order_LUT.txt
$ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta
$ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta --regheader
--seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --km-ref
8 47 --o gtmpvc.output

Also I checked the run of gtmseg via "*tkmeditfv*" where i can visualise 258
Head-ExtraCerebral, and additionally I checked *gtmseg.ctab *file also 258
Head-ExtraCerebral in the list.

I will be happy to hear from you.
Kind regards.
-- 
Ph.D. Bahar Hazal Yalçınkaya
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