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Hi Doug, thank you for your reply! When I look at my surface-projected non-pvc data per subject, initially it seemed as there were a lot of values zero, but when I go to configure > and replace the threshold to 0, the whole surface is covered with non-zero pet values, as would be expected. Hence, I do not understand why the stacking of these images over all subjects gives me an almost empty mask.mgh (only about 1500 vertices with a pet value left) and thus an almost empty stacked 4D pet file.

This is my command for projection of the non-pvc data: mri_vol2surf --mov ${in_dir}/${session}.gtmnopvc.output.pons/mgx.ctxgm.nii.gz --reg ${in_dir}/${session}.gtmnopvc.output.pons/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 \ --o ${in_dir}/lh.mgx.ctxgm.${session}.fsaverage.sm00.nopvc.pons.nii.gz --cortex --trgsubject fsaverage

for the stacking, I am using: mri_concat --f "$lhmgxctxgm" --prune --o ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm00.nopvc.pons.nii.gz

When I omit the prune flag with the mri_concat, I get a good result.

Do you recognize any issues here? Thank you! best regards Julie

On Thu, 14 Jan 2021 at 10:57, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

A 0 value usually indicates a bad or uninterpretable voxel which you would not want to include in your analysis. You can, of course, by not pruning. But I think you need to answer the question as to why the values are 0. Is 0 interpretable in this case?

On 1/11/2021 6:15 PM, Julie Ottoy wrote:

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Dear Doug,

I was wondering why the flag --prune is recommended (petsurfer website) when creating a stacked pet file and during surface-smoothing. If I understood correctly, this would set all vertices that are 0 in at least one subject to 0 ("set vox to 0 unless all frames are non-zero")? In my non-pvc data, it seems as though a lot of the surface-projected values are 0. Hence, when I perform a surface-based regression between PET and a regressor and I use the --prune flag during mri_concat, I don't get any results.

Thank you! best regards Julie

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Hi Doug,

Thanks. Yeah I am sure. I went through all my subjects with the time button. Could it potentially be an internal rounding issue (almost all my pet values are between 0 and 1, so they are put to 0?) Most likely not, but still not sure what's happening!

On Fri, 15 Jan 2021 at 09:27, Douglas N. Greve dgreve@mgh.harvard.edu wrote:

Are you sure that there is not one subject that has a bunch of 0s? All it would take is one. You can also look at a "time course" of your subjects by clicking on the time course button in freeview

On 1/14/2021 11:38 AM, Julie Ottoy wrote:

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Hi Doug, thank you for your reply! When I look at my surface-projected non-pvc data per subject, initially it seemed as there were a lot of values zero, but when I go to configure > and replace the threshold to 0, the whole surface is covered with non-zero pet values, as would be expected. Hence, I do not understand why the stacking of these images over all subjects gives me an almost empty mask.mgh (only about 1500 vertices with a pet value left) and thus an almost empty stacked 4D pet file.

This is my command for projection of the non-pvc data: mri_vol2surf --mov ${in_dir}/${session}.gtmnopvc.output.pons/mgx.ctxgm.nii.gz --reg ${in_dir}/${session}.gtmnopvc.output.pons/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 \ --o ${in_dir}/lh.mgx.ctxgm.${session}.fsaverage.sm00.nopvc.pons.nii.gz --cortex --trgsubject fsaverage

for the stacking, I am using: mri_concat --f "$lhmgxctxgm" --prune --o ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm00.nopvc.pons.nii.gz

When I omit the prune flag with the mri_concat, I get a good result.

Do you recognize any issues here? Thank you! best regards Julie

On Thu, 14 Jan 2021 at 10:57, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

...

A 0 value usually indicates a bad or uninterpretable voxel which you would not want to include in your analysis. You can, of course, by not pruning. But I think you need to answer the question as to why the values are 0. Is 0 interpretable in this case?

On 1/11/2021 6:15 PM, Julie Ottoy wrote:

    External Email - Use Caution

Dear Doug,

I was wondering why the flag --prune is recommended (petsurfer website) when creating a stacked pet file and during surface-smoothing. If I understood correctly, this would set all vertices that are 0 in at least one subject to 0 ("set vox to 0 unless all frames are non-zero")? In my non-pvc data, it seems as though a lot of the surface-projected values are 0. Hence, when I perform a surface-based regression between PET and a regressor and I use the --prune flag during mri_concat, I don't get any results.

Thank you! best regards Julie

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