BIDs configuration file: Difference between revisions

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==BIDs configuration file==
==BIDs configuration file==


BIDs configuration file is used to specify the naming convention for your data file in 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.
 
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 which specified when you run the setup_subject_3 script.
(So "sub-SUBJ" will be "sub-1234" in case the subject ID is "1234" as the result file name)
 
The "Name" part in "sub-SUBJ_Name" should be replace by the text you want to use following the [https://bids.neuroimaging.io/ BIDs format] rules.
 
====Example:====
 
gre_fieldmap_5 sub-'''SUBJ'''_fmap_mag
gre_fieldmap_6 sub-'''SUBJ'''_fmap_phase
MPRAGE_15 sub-'''SUBJ'''_mprage
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
MPRAGE_6.4_min__0.8X0.8X0.8mm_7 sub-'''SUBJ'''_T1w_rec-uncorrected
 
 
<!--====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 18:32, 28 October 2019

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 which specified when you run the setup_subject_3 script. (So "sub-SUBJ" will be "sub-1234" in case the subject ID is "1234" as the result file name)

The "Name" part in "sub-SUBJ_Name" should be replace by the text you want to use following the BIDs format rules.

Example:

gre_fieldmap_5 sub-SUBJ_fmap_mag
gre_fieldmap_6 sub-SUBJ_fmap_phase
MPRAGE_15 sub-SUBJ_mprage
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
MPRAGE_6.4_min__0.8X0.8X0.8mm_7 sub-SUBJ_T1w_rec-uncorrected