External Email - Use Caution 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 <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing#LongitudinalProcessing51.LongitudinalStream.28recon-all-long.29>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 <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLVBM/UserGuide#C_-_Creating_the_template:_fslvbm_2_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
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