External Email - Use Caution
Sure I try, thank you for the replay.
I'm using the above-mentioned analisis to obtain the Uptake for the region
in Desikan atlas, but the results are strange.
I think the error is in the last command but I'm not sure.
The first time I had used mri command without --psf FWHM to not use Partial
volume correction.
mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta
--seg gtmseg100.mgz --no-rescale --auto-mask 1 .01 --mgx .01 --o
$GTM_DIR/gtmpvc_PET.output
But the result in gtm.stats.dat have some region ( those region with less
voxel) with negative Uptake. Physically inconsistent but I had thought the
problem was in the tissue fraction effect.
The second command uses the --no-tfe option like indicated in the wiki
page, buth instead of negative count it returns high counts iven in regions
indicated with 0 voxel. Again Physically inconsistent.
I tried different combination of the option to --auto-mask ang --mgx but
it's not work differently or not at all.
I don't have an idea of what and how the problem is, and not even where I
can study to find the correct application metod.
Thank you for any suggestions you can give me.
Il giorno mar 26 set 2023 alle ore 16:03 Douglas N. Greve <
dgr...@mgh.harvard.edu> ha scritto:
> External Email - Use Caution
>
> I'm not sure what problem you are describing. Can you elaborate?
>
> On 9/25/2023 9:16 AM, Matteo Parodi wrote:
>
> External Email - Use Caution
> Hello,
>
> I'm trying to perform a pet ROI analysis on an image recon from a T1.
> I have to perform the analysis without normalization and partial volume
> correction.
> I'm having problems with regions with few or no voxels which makes me
> think I'm doing the analysis completely wrong .
>
> With this command I obtain negative values for these regions:
>
> mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg
> ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1
> .01 --mgx .01 --o $GTM_DIR/gtmpvc_PET.output
>
> While with this I get many counts even for regions without voxels:
>
> mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg
> ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask
> 1.01 --no-tfe --o $GTM_DIR/gtmpvc_PET.output
>
> Could you help me understand my mistake.
> Thank you very much.
> Parodi Matteo.
>
>
>
>
>
>
> I will insert the commands I used before the ROI analysis:
>
> recon-all -s Subj -i $IMAGED -all -threads 10
>
> gtmseg --keep-cc --s Subj --xcerseg --o gtmseg100.mgz
>
> mri_coreg --s Subj --mov ${SUBJECTS_DIR}/PET.nii.gz --reg
> ${SUBJECTS_DIR}/PET.reg.lta --threads 10
>
>
>
>
>
>
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