diff --git a/README.md b/README.md index 9d67d8f..cdb39ae 100644 --- a/README.md +++ b/README.md @@ -25,11 +25,15 @@ This App has the following command line arguments: $ docker run -ti --rm bids/freesurfer --help usage: run.py [-h] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] + [--session_label SESSION_LABEL [SESSION_LABEL ...]] [--n_cpus N_CPUS] - [--stages {autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon2-pial,autorecon3,autorecon-all,all} - [{autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon2-pial,autorecon3,autorecon-all,all} ...]] - [--template_name TEMPLATE_NAME] --license_key LICENSE_KEY + [--stages {autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon-pial,autorecon3,autorecon-all,all} + [{autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon-pial,autorecon3,autorecon-all,all} ...]] + [--steps {cross-sectional,template,longitudinal} + [{cross-sectional,template,longitudinal} ...]] + [--template_name TEMPLATE_NAME] --license_file LICENSE_FILE [--acquisition_label ACQUISITION_LABEL] + [--refine_pial_acquisition_label REFINE_PIAL_ACQUISITION_LABEL] [--multiple_sessions {longitudinal,multiday}] [--refine_pial {T2,FLAIR,None,T1only}] [--hires_mode {auto,enable,disable}] @@ -39,6 +43,7 @@ This App has the following command line arguments: [-v] [--bids_validator_config BIDS_VALIDATOR_CONFIG] [--skip_bids_validator] bids_dir output_dir {participant,group1,group2} + FreeSurfer recon-all + custom template generation. positional arguments: @@ -51,10 +56,10 @@ This App has the following command line arguments: {participant,group1,group2} Level of the analysis that will be performed. Multiple participant level analyses can be run independently - (in parallel) using the same output_dir. "goup1" - creates study specific group template. "group2 exports - group stats tables for cortical parcellation and - subcortical segmentation. + (in parallel) using the same output_dir. "group1" + creates study specific group template. "group2" + exports group stats tables for cortical parcellation, + subcortical segmentation a table with euler numbers. optional arguments: -h, --help show this help message and exit @@ -65,21 +70,34 @@ This App has the following command line arguments: parameter is not provided all subjects should be analyzed. Multiple participants can be specified with a space separated list. + --session_label SESSION_LABEL [SESSION_LABEL ...] + The label of the session that should be analyzed. The + label corresponds to ses- from the BIDS + spec (so it does not include "ses-"). If this + parameter is not provided all sessions should be + analyzed. Multiple sessions can be specified with a + space separated list. --n_cpus N_CPUS Number of CPUs/cores available to use. - --stages {autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon2-pial,autorecon3,autorecon-all,all} - [{autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon2-pial,autorecon3,autorecon-all,all} ...] + --stages {autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon-pial,autorecon3,autorecon-all,all} + [{autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon-pial,autorecon3,autorecon-all,all} ...] Autorecon stages to run. + --steps {cross-sectional,template,longitudinal} [{cross-sectional,template,longitudinal} ...] + Longitudinal pipeline steps to run. --template_name TEMPLATE_NAME Name for the custom group level template generated for this dataset --license_file LICENSE_FILE Path to FreeSurfer license key file. To obtain it you - need to register (for free) visit + need to register (for free) at https://surfer.nmr.mgh.harvard.edu/registration.html --acquisition_label ACQUISITION_LABEL If the dataset contains multiple T1 weighted images from different acquisitions which one should be used? Corresponds to "acq-" + --refine_pial_acquisition_label REFINE_PIAL_ACQUISITION_LABEL + If the dataset contains multiple T2 or FLAIR weighted + images from different acquisitions which one should be + used? Corresponds to "acq-" --multiple_sessions {longitudinal,multiday} For datasets with multiday sessions where you do not want to use the longitudinal pipeline, i.e., sessions @@ -100,15 +118,15 @@ This App has the following command line arguments: stats from. --measurements {area,volume,thickness,thicknessstd,meancurv,gauscurv,foldind,curvind} [{area,volume,thickness,thicknessstd,meancurv,gauscurv,foldind,curvind} ...] - Group2 option: cortical measurements to extract stats for. + Group2 option: cortical measurements to extract stats + for. -v, --version show program's version number and exit --bids_validator_config BIDS_VALIDATOR_CONFIG JSON file specifying configuration of bids-validator: See https://github.com/INCF/bids-validator for more info --skip_bids_validator - skips bids validation - + skips bids validation #### Participant level To run it in participant level mode (for one participant): @@ -125,6 +143,7 @@ To run it in participant level mode (for one participant): After doing this for all subjects (potentially in parallel) the group level analyses can be run. +##### Template creation To create a study specific template run: docker run -ti --rm \ @@ -134,8 +153,12 @@ To create a study specific template run: /bids_dataset /outputs group1 \ --license_file "license.txt" +##### Stats and quality tables export To export tables with aggregated measurements within regions of -cortical parcellation and subcortical segementation run: +cortical parcellation and subcortical segementation, and a table with + euler numbers (a quality metric, see + [Rosen et. al, 2017](https://www.biorxiv.org/content/early/2017/10/01/125161)) + run: docker run -ti --rm \ -v /Users/filo/data/ds005:/bids_dataset:ro \ @@ -143,4 +166,11 @@ cortical parcellation and subcortical segementation run: bids/freesurfer \ /bids_dataset /outputs group2 \ --license_file "license.txt" -Also see *--parcellations* and *--measurements* arguments. +Also see the *--parcellations* and *--measurements* arguments. + +This step writes ouput into `/00_group2_stats_tables/`. E.g.: + +* `lh.aparc.thickness.tsv` contains cortical thickness values for the +left hemisphere extracted via the aparac parcellation. +* `aseg.tsv` contains subcortical information from the aseg segmentation. +* `euler.tsv` contains the euler numbers \ No newline at end of file