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Hi Bruce,
Thanks for your answer! Before seeing this warning (rather: error, as no output is produced), I'd not have thought the pre-post images have different geometries, as I'm pretty sure their acquisition parameters were the same. The pre and post of any one subject, as well as the different subjects' images, all seem to have identical voxel size (1x1x1) and image size (176x224x160). Furthemore, the (0,0,0) point seems to always overlap well-enough on the anterior commissure...
This all suggests to me the geometry differences are trivial, so the resampling is worth a try. However, I'm unsure whether, in the call to *mri_convert -rl*, the target would have to be subject-specific (e.g. resample each 'post' to the 'pre' baseline), or if I should use a single target for all the pre&post images in the study, a bit like the study-specific template https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLVBM/UserGuide#C_-_Creating_the_template:_fslvbm_2_template used by VBM?
Cheers, Tudor
On 6 June 2018 at 16:37, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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 CautionHello, 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 tudor3@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:
- 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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