BIDS beginner - convert data to BIDS format

1

Hi there,

I might need some support to convert my data to the BIDS format. Specifically, I am currently having a hard time understanding the type of data to be included in the “anat” subfolder. Specifically, what does “inplane” t1 and t2 refer to? In my data, I have my mprage, and EPI task. In other words, is it ok to only input my de-identified mprage in “anat” and epi task (+events) in “func”?

Also, I am currently trying to use mri-deface, but when I try to execute the following inline “./mri_deface sample_T1_input.mgz talairach_mixed_with_skull.gca face.gca sample_T1_input_defaced.mgz” Terminal says: “-bash: ./mri_deface: Permission denied”

Thank you for your help!
Damien

2

In plane sequences are a bit of a relict of the past. In your case you should provide (at least):

  • sub-*/anat/sub-*_T1w.nii.gz
  • sub-*/func/sub-*_bold.nii.gz
  • sub-*/func/sub-*_events.tsv
  • sub-*/func/sub-*_bold.json

The validator will guide you from there if you have missing or inconsistent files.

I think this is the problem you are running into: https://unix.stackexchange.com/questions/203371/run-script-sh-vs-bash-script-sh-permission-denied

3

Perfect!

-> mri-deface work perfectly
-> is there an equivalent to “dcm2niigui” but for converting Dicom to json?

thanks again

4

For DICOM to nifti/json conversion I would recommend using dcm2niix from the command line.

5

OK. let say that my Dicom file for the EPI task is under a Folder named “EPI_TASK_0005” what is the exact command line to extract dicom to json using dcm2niix?

6

Also, my DICOM files are under an .IMA extension

EPI_TASK_0005/
R_B_G_MR.BRAIN_RESEARCH_3T_PSYCHIATRIE.0005.0001.2017.05.11.13.48.35.492846.399983946.IMA
…

7

A GUI wrapper for dcm2niix is provided with MRIcroGL - choose the “Convert DICOM to NIfTI” menu item from the “Import” menu. The GUI not only converts your data, but it shows you the resulting terminal command as well. Therefore, you can get used to the graphical interface and then easily copy and paste your desired conversion into a script. If you prefer Matlab, the dicm2nii provides a nice graphical interface.

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8

it worked perfectly! thank you so much!

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