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. < 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 CautionDear 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1h9TaaGM0shk3pzyFd7Y9YQIwpTwy5oZ93L8lWYf1AFBqWe...