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 [[Scripts: | 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- | Original_File_Name sub-'''SUBJ'''_Name | ||
Original_File_Name sub- | Original_File_Name sub-'''SUBJ'''_Name | ||
Original_File_Name sub- | 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 which specified when you run the setup_subject_3 script. | '''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) | (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:==== | ====Example:==== | ||
gre_fieldmap_5 sub- | gre_fieldmap_5 sub-'''SUBJ'''_fmap_mag | ||
gre_fieldmap_6 sub- | gre_fieldmap_6 sub-'''SUBJ'''_fmap_phase | ||
MPRAGE_15 sub- | MPRAGE_15 sub-'''SUBJ'''_mprage | ||
Task_Block_1_9 sub- | Task_Block_1_9 sub-'''SUBJ'''_task1 | ||
Task_Block_2_10 sub- | Task_Block_2_10 sub-'''SUBJ'''_task2 | ||
MPRAGE_6.4_min__0.8X0.8X0.8mm_8 sub- | MPRAGE_6.4_min__0.8X0.8X0.8mm_8 sub-'''SUBJ'''_T1w | ||
MPRAGE_6.4_min__0.8X0.8X0.8mm_7 sub- | 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