[Freesurfer] psf formula PET SURFER

2024-02-18 Thread Federica Di Antonio 
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Dear experts,

I'm employing PETsurfer for partial volume correction.
Could you share the definition or formula you use to define the psf (flag
--psf of mri_gtmpvc) that is used to correct the PET image?
I understand that it is an isotropic gaussian filter, but could you maybe
provide the precise formula you employ or the reference you refer to?

Thank you so much for your kindness and availability,

Federica Di Antonio
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[Freesurfer] PETsurfer: PVC without psf of the scanner

2022-12-12 Thread Federica Di Antonio 
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Dear experts,



Few weeks ago i wrote to this mailing list but I didn't receive any answer,
so I'll try again:


mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz

 --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output


If I put psf to 0, there is no PVC, and the same happens if I don’t
put that flag at all.t all

Is able mri_gtmpvc to evaluate the fwhm without receiving it from the user?

I apologize for the repetition,

Thanks for your patience,


Federica
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[Freesurfer] cvs clarifications with petsurfer

2023-02-17 Thread Federica Di Antonio 
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Dear Freesurfer experts,

I'm using PETsurfer. I've done the standard pipeline for all my subjects,
using the cvs registration.
I was wondering (maybe it's very stupid) when the standard pipeline "uses"
the cvs resulting files (except for subcortical volume-based analysis and
final resampling).

Moreover, when I obtain a resampled file (like subctxgm.cvs.2mm.sm00.nii.gz
) should I process it with freesurfer?

Sorry for my english, maybe what I ask is not very clear, but I hope you
can help me.
Thank you so much for your time and kindness!

Sincerely,
Federica
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[Freesurfer] different results for gtmpvc with different tracers

2023-02-17 Thread Federica Di Antonio 
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Dear experts,

I hope this email finds you well.
I run the pvc correction with mri_gtmpvc for subjects data obtained with
two different PET tracers.
In gtm.stats.dat, for every subject and every region, the number of voxels
evaluated for amyloid tracer is approximately twice the volume evaluated
for the second tracer.
I'd expect that the volume of a region for the same subject doesn't change
with the tracer.

Do you think this error can result from previous errors in the analysis? Or
is it in some way plausible?

Thank you for your patience,
Federica
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Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

2023-02-27 Thread Federica Di Antonio 
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Thank you so much!



Il giorno gio 15 dic 2022 alle ore 16:24 Douglas N. Greve <
dgr...@mgh.harvard.edu> ha scritto:

> I have something called the adaptive GTM that is currently a "hidden"
> feature in mri_gtmpvc as it has not been published yet. You can try it by
> adding the following flags --opt 1 --opt-tol 4 10e-6 .02 --opt-seg-merge
> When this is done, there will be a file called gtmdir/aux/opt.params.dat
> The value in that file with be the fwhm. Run mri_gtmpvc again passing that
> value as the --psf
> Again, this has not been fully evaluated so use at your own risk.
>
>
> On 12/12/2022 3:10 AM, Federica Di Antonio wrote:
>
> External Email - Use Caution
>
> Dear experts,
>
>
>
> Few weeks ago i wrote to this mailing list but I didn't receive any
> answer, so I'll try again:
>
>
> mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
>
>  --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output
>
>
> If I put psf to 0, there is no PVC, and the same happens if I don’t put that 
> flag at all.t all
>
> Is able mri_gtmpvc to evaluate the fwhm without receiving it from the user?
>
> I apologize for the repetition,
>
> Thanks for your patience,
>
> Federica
>
>
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Re: [Freesurfer] different results for gtmpvc with different tracers

2023-03-15 Thread Federica Di Antonio 
External Email - Use Caution

of course: I run the same line of command for both amyloid and tau pet
images with a fwhm = 1 in order to see what have happened

mri_gtmpvc --i taupet.nii --reg tau.reg.lta --psf 1 --seg gtmseg.mgz
--auto-mask 1 .01 --mgx .01 --no-rescale  --o tau.output

mri_gtmpvc --i amypet.nii --reg amy.reg.lta --psf 1 --seg gtmseg.mgz
--auto-mask 1 .01 --mgx .01 --no-rescale  --o amy.output

when I extract gtm.stats.dat file and I compare the number of voxels for
the same regions (and for the same subject of course) I obtain these values
(attached files). Can I suppose this effect descends from the flag
--automask? maybe the different automatic masks lead to different pixel
size.. I don't know, I would be very grateful for any information.
Thanks for all the help you can give me about; sincere greetings from

Federica Di Antonio

Il giorno lun 6 mar 2023 alle ore 16:31 Douglas N. Greve <
dgr...@mgh.harvard.edu> ha scritto:

> can you send an example?
>
> On 2/17/2023 9:38 AM, Federica Di Antonio wrote:
>
> External Email - Use Caution
> Dear experts,
>
> I hope this email finds you well.
> I run the pvc correction with mri_gtmpvc for subjects data obtained with
> two different PET tracers.
> In gtm.stats.dat, for every subject and every region, the number of voxels
> evaluated for amyloid tracer is approximately twice the volume evaluated
> for the second tracer.
> I'd expect that the volume of a region for the same subject doesn't change
> with the tracer.
>
> Do you think this error can result from previous errors in the analysis?
> Or is it in some way plausible?
>
> Thank you for your patience,
> Federica
>
>
> ___
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1_AMY_VOL_NEW.dat
Description: Binary data


1_TAU_VOL_NEW.dat
Description: Binary data
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[Freesurfer] negative uptakes after GTM pvc correction

2023-03-21 Thread Federica Di Antonio 
External Email - Use Caution

Dear experts,

I report an answer you gave about some negative values avatar partial
volume correction:

"[...] Usually this only happens in small ROIs and/or low uptake regions.
Why might the model not be perfect? It could be a number of things:

1. the MRI-PET registration is inaccurate
2. the MRI segmentation is inaccurate

3. the ideal segmentation is not reflected by the MRI segmentation (eg, one
of the segmentations has a hot spot)"

I wonder if it is possible for you to give me an hint about the reason why
an inaccurate registration or segmentation can cause negative uptake
values. At first sight it seemed intuitive to me, but on second thought
that's not so obvious.

I would be very grateful for any help!

Federica Di Antonio
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[Freesurfer] mri_cvs_register cost function

2023-03-24 Thread Federica Di Antonio 
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Dear experts,

May I ask you which cost function is used by mri_cvs_register?
Thank you so much for your support!

Federica Di Antonio
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[Freesurfer] negative uptakes after GTM pvc correction

2023-03-24 Thread Federica Di Antonio 
External Email - Use Caution

Dear experts,

I report an answer you gave about some negative values avatar partial
volume correction:

"[...] Usually this only happens in small ROIs and/or low uptake regions.
Why might the model not be perfect? It could be a number of things:

1. the MRI-PET registration is inaccurate
2. the MRI segmentation is inaccurate

3. the ideal segmentation is not reflected by the MRI segmentation (eg, one
of the segmentations has a hot spot)"

I wonder if it is possible for you to give me an hint about the reason why
an inaccurate registration or segmentation can cause negative uptake
values. At first sight it seemed intuitive to me, but on second thought
that's not so obvious.

I would be very grateful for any help!

Federica Di Antonio
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Re: [Freesurfer] mri_cvs_register cost function

2023-03-27 Thread Federica Di Antonio 
External Email - Use Caution

Thank you so much Lilla!

Il lun 27 mar 2023, 17:54 Zollei, Lilla,Ph.D.  ha
scritto:

> Hi Federica,
>
> There are two registration steps in cvs_register. One is the surface-based
> registration step that aligns the curvature patterns of the inputs, and the
> volumetric registration step that, by default, uses SSE (sum of squared
> errors)
>
> Best, Lilla
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Federica Di Antonio <
> fedediantoni...@gmail.com>
> *Sent:* Friday, March 24, 2023 5:37 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] mri_cvs_register cost function
>
>
> External Email - Use Caution
>
> Dear experts,
>
> May I ask you which cost function is used by mri_cvs_register?
> Thank you so much for your support!
>
> Federica Di Antonio
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>
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Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

2023-05-08 Thread Federica Di Antonio 
External Email - Use Caution

Dear experts,
I am here again because I'd like to  ask a specification about the fwhm
that the alghoritm evaluates: the main value that I obtained was 7.3 mm; It
is an high value for a pv correction.
May I put in half the value?
Because I wonder if the definition of fwhm used by mri_gtmpvc was different
from mine.

Thenk you so much for your availability,

Federica Di Antonio

Il giorno lun 27 feb 2023 alle ore 14:30 Federica Di Antonio <
fedediantoni...@gmail.com> ha scritto:

> Thank you so much!
>
>
>
> Il giorno gio 15 dic 2022 alle ore 16:24 Douglas N. Greve <
> dgr...@mgh.harvard.edu> ha scritto:
>
>> I have something called the adaptive GTM that is currently a "hidden"
>> feature in mri_gtmpvc as it has not been published yet. You can try it by
>> adding the following flags --opt 1 --opt-tol 4 10e-6 .02 --opt-seg-merge
>> When this is done, there will be a file called gtmdir/aux/opt.params.dat
>> The value in that file with be the fwhm. Run mri_gtmpvc again passing that
>> value as the --psf
>> Again, this has not been fully evaluated so use at your own risk.
>>
>>
>> On 12/12/2022 3:10 AM, Federica Di Antonio wrote:
>>
>> External Email - Use Caution
>>
>> Dear experts,
>>
>>
>>
>> Few weeks ago i wrote to this mailing list but I didn't receive any
>> answer, so I'll try again:
>>
>>
>> mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
>>
>>  --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output
>>
>>
>> If I put psf to 0, there is no PVC, and the same happens if I don’t put that 
>> flag at all.t all
>>
>> Is able mri_gtmpvc to evaluate the fwhm without receiving it from the user?
>>
>> I apologize for the repetition,
>>
>> Thanks for your patience,
>>
>> Federica
>>
>>
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Re: [Freesurfer] different results for gtmpvc with different tracers

2023-06-09 Thread Federica Di Antonio 
External Email - Use Caution

That's right!
tau PET images has z voxel dimension that is the double of amy PET voxel.

Thank you so much!

Il giorno lun 27 mar 2023 alle ore 15:49 Douglas N. Greve <
dgr...@mgh.harvard.edu> ha scritto:

> Do the two inputs have different voxel sizes? The gtm.stats.dat file
> reports the number of voxels so if the volumes have different voxels sizes,
> you will get different values out. If this is not the source of the
> problem, please send the gtm.stats files.
>
> On 3/15/2023 4:06 AM, Federica Di Antonio wrote:
>
> External Email - Use Caution
> of course: I run the same line of command for both amyloid and tau pet
> images with a fwhm = 1 in order to see what have happened
>
> mri_gtmpvc --i taupet.nii --reg tau.reg.lta --psf 1 --seg gtmseg.mgz
> --auto-mask 1 .01 --mgx .01 --no-rescale  --o tau.output
>
> mri_gtmpvc --i amypet.nii --reg amy.reg.lta --psf 1 --seg gtmseg.mgz
> --auto-mask 1 .01 --mgx .01 --no-rescale  --o amy.output
>
> when I extract gtm.stats.dat file and I compare the number of voxels for
> the same regions (and for the same subject of course) I obtain these values
> (attached files). Can I suppose this effect descends from the flag
> --automask? maybe the different automatic masks lead to different pixel
> size.. I don't know, I would be very grateful for any information.
> Thanks for all the help you can give me about; sincere greetings from
>
> Federica Di Antonio
>
> Il giorno lun 6 mar 2023 alle ore 16:31 Douglas N. Greve <
> dgr...@mgh.harvard.edu> ha scritto:
>
>> can you send an example?
>>
>> On 2/17/2023 9:38 AM, Federica Di Antonio wrote:
>>
>> External Email - Use Caution
>> Dear experts,
>>
>> I hope this email finds you well.
>> I run the pvc correction with mri_gtmpvc for subjects data obtained with
>> two different PET tracers.
>> In gtm.stats.dat, for every subject and every region, the number of
>> voxels evaluated for amyloid tracer is approximately twice the volume
>> evaluated for the second tracer.
>> I'd expect that the volume of a region for the same subject doesn't
>> change with the tracer.
>>
>> Do you think this error can result from previous errors in the analysis?
>> Or is it in some way plausible?
>>
>> Thank you for your patience,
>> Federica
>>
>>
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