Merge pull request #67 from arnaudbore/new_validate_bids_structure

Add possibility to have full AP-PA LR-RL data
scilus · Dec 1, 2022 · 5f1c2ec · 5f1c2ec
2 parents 9ba7512 + 9e3ea94
commit 5f1c2ec
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diff --git a/USAGE b/USAGE
@@ -37,6 +37,8 @@ DESCRIPTION
 
     --bids=/path/to/[bids]              BIDS folder following the BIDS convention.
 
+    --fs=/path/to/[fs]                  Freesurfer output folder.
+
     --bids_config                       BIDS configuration file in json pre-generated by TractoFlow(Read_BIDS process).
                                         This option must be used only if --bids did not work due to an issue in the BIDS
                                         folder.
@@ -109,9 +111,10 @@ OPTIONAL ARGUMENTS (current value)
 
 --fa                                        Initial FA threshold to compute the frf ($fa).
 --min_fa                                    Minimum FA threshold to compute the frf ($min_fa).
+--min_nvox                                  Minimum number of voxels to compute the frf ($min_nvox).
 --roi_radius                                Region of interest radius to compute the frf ($roi_radius).
 --set_frf                                   Set manually the frf ($set_frf).
---manual_frf                                FRF set manually ($manual_frf).
+--manual_frf                                FRF set manually (--manual_frf "$manual_frf").
 
 --mean_frf                                  Mean the frf of all subjects ($mean_frf).
                                             USE ONLY IF ALL OF SUBJECTS COME FROM THE SAME SCANNER
@@ -208,7 +211,8 @@ cbrain                                      When this profile is used, Nextflow
 
 ABS                                         When this profile is used, TractoFlow-ABS (Atlas Based Segmentation) is used.
                                             This profile must be used for pathological data.
-                                            The aparc+aseg.nii.gz and wmparc.nii.gz must be in the same space than t1.nii.gz
+                                            The aparc+aseg.nii.gz and wmparc.nii.gz must be in the same space than t1.nii.gz.
+                                            In order to use BIDS, either use the root structure or bids and freesurfer structures.
 
 bundling                                    When this profile is used, it will activate custom tracking parameters to improve recobundle results.
                                             Local tracking will be enable with fa seeding mask and tracking mask.