External Email - Use Caution Quick follow-up note in case it will be helpful to anyone experiencing the same problem: I got hold of a Linux machine and installed FreeSurfer 6.0 on it; running these same commands there successfuly produced the norm.mgz file. Therefore, this appears to be a bug in FS v5.3.0 (which is sadly the only version available to run on Windows, using a Linux Virtual Machine). Cheers, Tudor
On Wed, 27 Jun 2018 at 18:00, Tudor Popescu <tud...@gmail.com> wrote: > Hi again, > > At a loss for more things to try here, I tried the following: for the > first subject in my sample, I replaced the 'post' scan (01_2.nii.gz) with a > copy of the pre (01_1.nii.gz ), to rule out the unlikely cause that an > actual geometries problem is at the root here, as reported in the > warning/error I mentioned earlier. > > While this removed the geometries message from the output of the base > command, the error about norm.mgz not being there remained. Further > searches of the FS mailing list revealed that this file's absence might be > due to a bug in FS v6 (even though I am running 5.3.0, through > VirtualBox, on Windows). Nevertheless, I followed the instructions > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57033.html>for > applying the bugfix patch, but when I redid everything (deleted subject > folders, reissued the commands), the result was the same. > > It thus seems the base step expects norm.mgz to exist, whereas the > previous steps ('-i' and 'cross') do not create it. > > I attach the recon-all logs for the pre, post and base of subject 01. > Would remain thankful to anyone who can suggest what else I can try! > > Best wishes, > Tudor > > On Thu, 21 Jun 2018 at 10:16, Tudor Popescu <tud...@gmail.com> wrote: > >> 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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