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updated usage and more info about group2 in examples
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@fliem
fliem committed Nov 30, 2017
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Expand Up @@ -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}]
Expand All @@ -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:
Expand All @@ -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
Expand All @@ -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-<session_label> 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-<acquisition_label>"
--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-<acquisition_label>"
--multiple_sessions {longitudinal,multiday}
For datasets with multiday sessions where you do not
want to use the longitudinal pipeline, i.e., sessions
Expand All @@ -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):
Expand All @@ -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 \
Expand All @@ -134,13 +153,24 @@ 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 \
-v /Users/filo/outputs:/outputs \
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 `<output_dir>/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

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