Center for Cognitive Neuroscience - User contributions [en]

BIDs configuration file

2019-10-18T21:42:05Z

Yan: /* More complicated format example: */

==BIDs configuration file==

BIDs configuration file is used to specify the naming convention for your data file in [[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" here should be replace by the name 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-120_T1w
MPRAGE_6.4_min__0.8X0.8X0.8mm_7 sub-120_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

BIDs configuration file

2019-10-18T21:40:32Z

Yan: /* Example: */

==BIDs configuration file==

BIDs configuration file is used to specify the naming convention for your data file in [[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" here should be replace by the name 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-120_T1w
MPRAGE_6.4_min__0.8X0.8X0.8mm_7 sub-120_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

BIDs configuration file

2019-10-18T21:06:15Z

Yan:

==BIDs configuration file==

BIDs configuration file is used to specify the naming convention for your data file in [[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" here should be replace by the name 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-120_T1w
MPRAGE_6.4_min__0.8X0.8X0.8mm_7 sub-120_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

Hoffman2:Scripts:setup subject 3

2019-10-17T20:27:36Z

Yan:

==Setup_subject script usage==
Setup_subject_3 (also named as setup_subject_bids) is built on top of setup_subject_2. The major goal is to apply BIDs format on the data structure. Besides of using BIDs structure, it added other useful features as well.

Setup_subject_3 has all the functions which exist in setup_subject_2 and works the same way with the same options as setup_subject_2.

===Basic Usage:===
setup_subject_3 [option] basedir subjectID

basedir is where you want the processed data to be stored in your Hoffman account,

subjectID is the subject folder name which has your subject Dicom data

===Options:===
--download hostname,userid,path
download data from Dicom server to you hoffman account
It requires 3 argument, separated by comma(,)
(If you have downloaded the data already, this option is not needed)

1. hostname - (ccn for ccn Dicom server, bmap for BMC Dicom server).
2. userid: Your Dicom server user ID
3. path: path to your data in dicom server

-d (or --do) : this option to specify the processing you want to add
After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: submit the job in batch mode

(Using option diags requires mcflirt, bet and melodic to be processed first)

-s (or --skip)
this option to specify the processing you want to skip
mcflirt : run mcflirt
bet : run bet
melodic : run melodic
diags : run diagnostics
mprage : process anatomical scans
sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_* command

--spm
Set SPM compatability

--bids
Bids format: specify using bids structure to group result files. However this option often being used with --config option to choose configuration file.
Without configuration file, the name conversion might not be correct under BIDs format rule.

--config FILEPATH/FILENAME
Specifying the bids naming configuration file path and name. Users should generate this file based on their data and Bids formatting rule. However there are sample files.

--sessdir ses-NN
Specify session directory name. This is for Bids format mode and when the data has multiple sessions. When you want the results all go into a session directory named ses-NN (NN represents session number, e.g. 02)

--notar
No compression of dicom/ folder. Normally raw dicom data will be compressed into dicom*.tar.gz at the end of NiFTI convert. With this option, it will not compress.
This option is good when you know you want to run the setup_subject_3 script again and want to save time on compression and decompression of the data.
You should run without this option on the last run so it will save the disk usage.

--setgrp GROUPNAME
Force the data's group to be set as the GROUPNAME specified. The GROUPNAME need to be an existing valid group name in Hoffman.

===Examples: ===

Load the script module first:
module load ccnscripts

Download data and run NIFTI convert
setup_subject_3 --download ccn,dicomuserid,/dicom/data/YOURGROUP/ basedir subjectID
( /dicom/data/YOURGROUP/subjectID should be where the raw data is located and accessable by your Dicom server user account)

Download data and run NIFTI convert and other FSL processing:
setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID

Process data only without download
setup_subject_3 -d mcflirt,bet,melodic,diags basedir subjectID
setup_subject_3 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
setup_subject_3 -d mprage basedir subjectID

Skip mcflirt,bet,melodic,diags
setup_subject_3 -s mcflirt,bet,melodic,diags basedir subjectID

===Notes===
Log File: provides useful details about what commands were run, their output and the script's status. It's located at

basedir/subjectID/notes/setup_log.date_numbers