Dear FS list,

( Apologies for asking my question again which I am still struggling to resolve and which I tried to clarify and condense below. )

I have pre and post-intervention data for a single group of subjects, and I'd like to extract the cortical thickness at both timepoints, for all standard regions in the atlas. I followed the standard approach for longitudinal studies, however the third ('base') step immediately gives this error:

"WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! "

I don't think the acquisition parameters of the pre-post images actually differ: I could verify that all images indeed have

- identical voxel size (1x1x1)

- identical image size (176x224x160)

- a (0,0,0) point that overlaps well-enough on the anterior commissure

This suggests trivial (if any) "geometry" differences, and at Bruce's suggestion, I used mri_convert to resample each subject's 'post' to their 'pre' baseline:

mri_convert -rl 01_1.nii.gz 01_2.nii.gz 01_2resampled.nii.gz

(and renamed the resampled file to 01_2). However, the base step,

recon-all -base 01 -tp 01_1 -tp 01_2 -all

still gives the same error about geometries, and also in addition, this one:

mghRead(/media/FS/01_1/mri/norm.mgz, -1): could not open file
MultiRegistration::loadMovables: could not open input volume /media/FS/01_1/mri/norm.mgz.

Inside /media/FS/01_1/mri/ (where /media/FS is my $SUBJECTS_DIR), there is indeed no norm.mgz, which suggests something in my previous commands for subject1:

recon-all -i 01_1.nii.gz -subjid 01_1
recon-all -i 01_2.nii.gz -subjid 01_2
recon-all -subjid 01_1 -all
recon-all -subjid 01_2 -all

..had gone wrong despite these having produced no errors. Although I thought the base step already does autorecon1 as part of the longitudinal pipeline, I tried doing it manually:

recon-all -autorecon1 -subjid 01

however this returns:

ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base: \' -base <templateid> -tp <tpNid> ... \'

..whereas running autorecon1 and 2 for the first timepoint instead,

recon-all -autorecon1 -autorecon2 -subjid 01_1

returns

mri_em_register: could not open input volume nu.mgz

Should I in fact use, in mri_convert -rl , a single target for all the pre&post images in the study, like the study-specific template used by VBM? Or what else can I try to get the base step to continue? I'm very grateful for any suggestions!

Cheers,

Tudor