blackhershey/enigma_ts_t1_pipeline

ENIGMA_TS structural imaging pipeline

ENIGMA_TS structural imaging pipeline

ENIGMA-TS pipelines to analyze structural brain MRI data (cortical and subcortical segmentation and quality control using FreeSurfer versions 6 and 7). This wrapper script fixes tksurfer command error (removed from latest FreeSurfer versions) and was put together by Yin Jin, integrating scripts provided by Sophia Thomopoulos and existing ENIGMA wrapper scripts and published ENIGMA pipelines. Further documentation available here. For questions please contact Yin Jin ([email protected]).

update 2_extractsubcortical_volumes.sh on 05/22/2022

Because Freesurfer version 6 and 7 variable names of subcortical volume are slightly different, we provide two transcripts (2_extractsubcortical_volumes_version6.sh and 2_extractsubcortical_volumes_version7.sh) to extract subcortical volumes.

Please check you Freesurfer version before running extractsubcortical_volumes transcript.

If you still have problem, feel free to contact me anytime ([email protected]).