BIDs configuration file: Difference between revisions

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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 sub-SUBJ_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 when you run the setup_subject_3 script.
'''SUBJ''' will be converted automatically to the subject ID
(So "sub-SUBJ" will be "sub-1234" in case the subject ID is "1234" as the result file name)
(For example, for subject ID "1234", "sub-SUBJ" will be changed to "sub-1234" )


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.
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
  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





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