From bd49b2c0c993c10a82eaaf15232fe1ce580737f8 Mon Sep 17 00:00:00 2001 From: Chris Filo Gorgolewski Date: Thu, 15 Feb 2018 17:36:25 -0800 Subject: [PATCH] fix invocations to include license binds --- README.md | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index cdb39ae..a12ef7e 100644 --- a/README.md +++ b/README.md @@ -134,9 +134,10 @@ To run it in participant level mode (for one participant): docker run -ti --rm \ -v /Users/filo/data/ds005:/bids_dataset:ro \ -v /Users/filo/outputs:/outputs \ + -v /Users/filo/freesurfer_license.txt:/license.txt \ bids/freesurfer \ /bids_dataset /outputs participant --participant_label 01 \ - --license_file "license.txt" + --license_file "/license.txt" #### Group level @@ -149,9 +150,10 @@ To create a study specific template run: docker run -ti --rm \ -v /Users/filo/data/ds005:/bids_dataset:ro \ -v /Users/filo/outputs:/outputs \ + -v /Users/filo/freesurfer_license.txt:/license.txt \ bids/freesurfer \ /bids_dataset /outputs group1 \ - --license_file "license.txt" + --license_file "/license.txt" ##### Stats and quality tables export To export tables with aggregated measurements within regions of @@ -163,9 +165,10 @@ cortical parcellation and subcortical segementation, and a table with docker run -ti --rm \ -v /Users/filo/data/ds005:/bids_dataset:ro \ -v /Users/filo/outputs:/outputs \ + -v /Users/filo/freesurfer_license.txt:/license.txt \ bids/freesurfer \ /bids_dataset /outputs group2 \ - --license_file "license.txt" + --license_file "/license.txt" Also see the *--parcellations* and *--measurements* arguments. This step writes ouput into `/00_group2_stats_tables/`. E.g.: @@ -173,4 +176,4 @@ 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 +* `euler.tsv` contains the euler numbers