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:
External Email - Use Caution
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.
<dgr...@mgh.harvard.edu <mailto:dgr...@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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