Hi Tudor
if you are sure that the differences are trivial you can resample the
images to all have exactly the same geometries and rerun (I think
mri_convert -rl <target vol> <source vol> <source vol resampled>
should do it (-rl is "reslice like"). If they are not trivial though you
may find effects that only reflect the acquisition differences.
cheers
Bruce
On Wed, 6 Jun 2018, Tudor Popescu wrote:
External Email - Use Caution
Hello,
If any more information is needed to address my question, please do let me
know. I hope to hear back and once again
thanks a lot for any assistance with this.
Best wishes,
Tudor
On 1 June 2018 at 16:07, Tudor Popescu <tud...@gmail.com> wrote:
Dear all,
I have pre and post-intervention data for a single group of subjects, and I'd
like to extract the cortical
thickness pre and post, for all standard regions in the atlas, and use those in
subsequent analyses.
Following the standard approach for longitudinal studies, I used the following
types of commands:
1. recon-all -i 01_1.nii.gz -subjid 01_1
recon-all -i 01_2.nii.gz -subjid 01_2
recon-all -i 02_1.nii.gz -subjid 02_1
..
where e.g. 01 is the subj code, and _1 and _2 represent pre and post scans
2. recon-all -subjid 01_1 -all
recon-all -subjid 01_2 -all
..
3. recon-all -base 01 -tp 01_1 -tp 01_2 -all
..
4. recon-all -long 01_1 01 -all
recon-all -long 01_2 01 -all
..
However, the base step has led to warnings of the type: "WARNING: Image
geometries differ across time, maybe
due to aquisition changes? This can potentially bias a longitudinal study! ",
and consequently to an empty
/stats folder -- even though my pre and post images are aligned and have
similar acquisition parameters.
Have I done something wrong, and how can I fix this warning/error? Many thanks
in advance for any help.
Best wishes,
Tudor
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