PR for eTIV fix and new stable release #413
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Consider local time formats when reading runtimes
fix intenstiy overflow in higher order interpolation in uchar
Fix: `imageio` bug
fix TypeError
Robustify `mris_info` string comparison to number of spaces (for FS741)
- get version tag from toml file - create versioned docker images for fastsurfer and tag the newest image as latest
- update code for version extraction
- get version tag from toml file - create versioned docker images for fastsurfer and tag the newest image as latest
- update code for version extraction
write Version to console as well make log dir before making log add .gitignore
Fix 'ondemand' bias field parameters in recon-surf
bump conda version
Change a cpu_count instance that was left to get_num_threads
…the Docker build script
Automatically find FastSurfer directories in the build script
…avoiding unexpected incompatibilities. Add documentation example (Example 6) for SLURM script. Fix some doc typos and Headlines. Remove/fix outdated documentation for --vol_segstats add .idea (pycham setings dir) to gitignore
Prepare/cleanup documentation for FastSurfer release
* Add script to create documented requirements files from docker/singularity image * fix docker --entrypoint and check for sif extension
* Fix documentation of messages in the slurm script
Fix the images-only default pattern "*.{mgz,nii,nii.gz}"
Increase the default time limit for the surface reconstruction
Fix some doc typos
Add --cpu_only and --skip_cleanup flags to srun_fastsurfer.sh with doc
* improve calculation of memory and cpus for requesting resources in slurm
* better estimation of subject folders from file names
fix cpus/ncpus typo
* Fix default values for memory and cores (and better handling)
Add check whether auto-generated work dir already exists
remove --ntasks-per-node, as that forces a scheduling on a single node.
Fix duplicated then in cleanup script
* add 3T atlas to talairach registration * add 3T atlas to pruned freesurfer installation * lower reference point of bfscaling is 1st percentile -> 3 (similar to freesurfer) * Add flags to switch to the 3T atlas for talairach registration. * Change target white matter intensity in N4_bias_correct.py to 105. * Update help text --------- Co-authored-by: Martin Reuter <[email protected]> Co-authored-by: diersk <[email protected]>
fix globbing, so globbing does happen if subjects/cases are read fix number of cpus per surf task (--hint=nomultithread makes sure hyperthreads are automatically allocated)
fix rescaledvol->rescalevol typo
fix typos in scripts
use nibabel read_geometry
Fix memory limitation and subject/case globbing on slurm script
…-options Add support for expert options for singularity.
Add apply_warp.py
"Small" changes to the CerebNet traning pipeline (missing apply_warp.py and shell errors in realistic_deformations)
- update READMEs for --3T flag - update recon_surf/README.md to mention that a biasfield corrected image will only be created, if none exists. - remove mentions of the reconsurf docker image in recon_surf/README.md - update READMEs to use brun_fastsurfer.sh for multiple subjects - update comments in Tutorials (--3T flag) - fix alternative bias-field correction in recon_surf (if no biasfield image [orig_nu.mgz]) is present - extend --parallel_subjects option in brun_fastsurfer.sh (to allow serial segmentation and parallel surfaces) - set version to 2.2.0 - set default subject_list splitter to = in srun_fastsurfer.sh to make it consistent with brun_fastsurfer.sh - reorder flags in srun_fastsurfer.sh --help and add --seg_only/--surf_only - add prepended subject_id in brun_fastsurfer.sh parallel mode
Update documentation for 2.2 Release
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This PR updates our stable branch to include recent fixes from dev for a new FastSurfer Release 2.2