We have organized the containers by the categories listed below. We are open to suggestions for better organization.
FreeSurfer rates a separate section because CNDA hosts several versions of the FreeSurfer container, and it is used extensively by the Benzinger Lab and others. The CNDA Help Desk does not have an opinion on which version of the FreeSurfer container is approriate for your work. This Free Surfer Tutorial from the Benzinger Labopen in new window provides instructions on how to run FreeSurfer from the command line as well as from an XNAT container.
Command Data Type Actions Version freesurfer-7-4-1 xnat:imageSessionData Run Freesurfer 7.4.1 on a session 1.2 freesurfer-7-4-1-relaunch fs:fsData Relaunch Freesurfer 7.4.1 after editing 1.2
Command Data Type Actions Version freesurfer-7-3-2 xnat:imageSessionData Run Freesurfer 7.3.2 on a session 1.2 freesurfer-7-3-2-relaunch fs:fsData Relaunch Freesurfer 7.3.2 after editing 1.2
Command Data Type Actions Version freesurfer-7-1-1 xnat:imageSessionData 7.1.1 on a session 1.0 freesurfer-7-1-1-relaunch fs:fsData Relaunch Freesurfer 7.1.1 after editing 1.0
Command Data Type Actions Version freesurfer-5-3-0-hcp-patch-relaunch fs:fsData Relaunch Freesurfer 5.3.0-HCP-patch after editing 1.0 freesurfer-5-3-0-hcp-patch xnat:imageSessionData Run Freesurfer 5.3.0-HCP-patch on a session 1.0
Command Data Type Actions Version freesurfer-snapshots fs:fsData Generate snapshots for FreeSurfer output 1.0
Command Data Type Actions Version adcortsig-roi-xnat fs:fsData AD Cortical Signature ROIs 1.0
Command Data Type Actions Version benice xnat:imageSessionData Run BENICE v1.31 1.31
Command Data Type Actions Version ilp-v2-xnat fs:fsData ILP v2.1 1.0
Command Data Type Actions Version manual-wmh-calcs manwmh:manwmhData Run Manual WMH Thresholding final calculations on a Manual WMH assessor 1.0 manual-wmh-preproc xnat:imageSessionData Run Manual WMH Thresholding preprocessing on a session that has a FLAIR scan in it 1.0
Command Data Type Actions Version mrfree-pet xnat:imageSessionData Run Jagust MR-Free PET processing workflow 1.0.5
Command Data Type Actions Version pet-unified-pipeline-fs xnat:imageSessionData Run PET Unified Pipeline (PUP) based on Freesurfer ROIs 1.4
Command Data Type Actions Version pet-unified-pipeline-manual xnat:imageSessionData Run PET Unified Pipeline (PUP) based on Manual (hand-drawn) ROIs 1.2
Command Data Type Actions Version 1-Scan-type Classifier 2-Registration xnat:imageSessionData Perform registration 1.0 3-Skullstrip xnat:imageSessionData Perform skullstrip 1.0 5-Prediction to patient-space xnat:imageSessionData: Convert prediction to patient_space 1.0 6-Patient-space to dcmseg xnat:imageSessionData Convert Patient-space nifti to dcmseg 1.0 7-Dcmseg to ROI-Assessor xnat:imageSessionData Upload prediction-DICOMSEG as ASSESSOR/ROI_COLLECTION 1.0
Command Data Type Actions Version register-mr xnat:imageScanData Run the RegisterMRToAtlas script on a scan 1.0
Command Data Type Actions Version tau-spatial-spread-xnat pup:pupTimeCourseData Tau Spatial Spread calculation 1.0
Command Data Type Actions Version ct_scan_classifier_usinggithub xnat:imageSessionData ct_scan_classifier_usinggithub 1.0
Command Data Type Actions Version dcm2niix-20Jul2022 xnat:imageScanData Run dcm2niix 20-Jul-2022 on a Scan 20Jul2022
Command Data Type Actions Version dcm2niix xnat:imageScanData Run dcm2niix 25-Nov-2018 on a Scan 25Nov18
Command Data Type Actions Version pup-4dfp-to-nifti-xnat pup:pupTimeCourseData PUP 4dfp to NIFTI conversion 1.0
Command Data Type Actions Version Other Dump Project xnat:projectData Run (dcm4che) dcmdump on a Project 2024.12.23 Documentation Grep Project xnat:projectData Run grep after dcmdump on a Project 2024.12.23 Documentation Dump Session xnat:imageSessionData Run dcmdump on a Session 2024.12.23 Documentation Project Manifest xnat:projectData List files or folders in a Project folder 2024.12.23 Documentation
