BIDs configuration file: Difference between revisions

From Center for Cognitive Neuroscience
Jump to navigation Jump to search
No edit summary
(24 intermediate revisions by 2 users not shown)
Line 1: Line 1:
==BIDs configuration file==
==BIDs configuration file==


BIDs configuration file is used to specify the naming convention for your data file in [[Scripts:setup subject 3]].
BIDs configuration file is used to specify the naming convention for your data file in [[Hoffman2:Scripts:setup_subject_3]].


This file should have the following format for all files you want to be converted to BIDs style names.
This file should have the following format for all files you want to be converted to BIDs style names.


  Original_File_Name sub-SUBJ_Name
  original_File_Name sub-'''SUBJ'''_Name
  Original_File_Name sub-SUBJ_Name
  original_File_Name sub-'''SUBJ'''_Name
  Original_File_Name sub-SUBJ_Name
  original_File_Name sub-'''SUBJ'''_Name
  ...
  ...


The Original_File_Name and the New_File_Name are separated by a space.
The original_File_Name and the sub-SUBJ_Name are separated by a space.
 
'''SUBJ''' will be converted automatically to the subject ID
(For example, for subject ID "1234", "sub-SUBJ" will be changed to "sub-1234" )
 
The "Name" in "sub-SUBJ_Name" should be replace by the string following the [https://bids.neuroimaging.io/ BIDs format] rules.


====Example:====
====Example:====


  gre_fieldmap_5 sub-SUBJ_fmap_mag
  gre_fieldmap_5 sub-'''SUBJ'''_fmap_magnitude
  gre_fieldmap_6 sub-SUBJ_fmap_phase
  gre_fieldmap_6 sub-'''SUBJ'''_fmap_phasediff
  MPRAGE_15 sub-SUBJ_mprage
  Task_Block_1_9 sub-'''SUBJ'''_task1
  Task_Block_1_9 sub-SUBJ_task1
  Task_Block_2_10 sub-'''SUBJ'''_task2
  Task_Block_2_10 sub-SUBJ_task2
  MPRAGE_6.4_min__0.8X0.8X0.8mm_8 sub-'''SUBJ'''_T1w
 
 
<!--====More complicated format example:====
 
For example you have multiple data with similar names and want to covert them all
 
BOLD_AP_Block01_13
BOLD_AP_Block02_16
BOLD_AP_Block03_19
BOLD_AP_Block03_22-->

Revision as of 18:01, 30 January 2020

BIDs configuration file

BIDs configuration file is used to specify the naming convention for your data file in Hoffman2:Scripts:setup_subject_3.

This file should have the following format for all files you want to be converted to BIDs style names.

original_File_Name sub-SUBJ_Name
original_File_Name sub-SUBJ_Name
original_File_Name sub-SUBJ_Name
...

The original_File_Name and the sub-SUBJ_Name are separated by a space.

SUBJ will be converted automatically to the subject ID (For example, for subject ID "1234", "sub-SUBJ" will be changed to "sub-1234" )

The "Name" in "sub-SUBJ_Name" should be replace by the string following the BIDs format rules.

Example:

gre_fieldmap_5 sub-SUBJ_fmap_magnitude
gre_fieldmap_6 sub-SUBJ_fmap_phasediff
Task_Block_1_9 sub-SUBJ_task1
Task_Block_2_10 sub-SUBJ_task2
MPRAGE_6.4_min__0.8X0.8X0.8mm_8 sub-SUBJ_T1w