How can I "gunzip the .nii.gz"?

Discussions
1

Hello,nice to meet you. This is Kikuko.

I started to use Brainstorm from 4 days before.
I’m trying to import MRI and surface in Brainstorm3 from Brainviza/Anatomist/Python.
At first, I tried to import them simply along with tutorial, but I coudn’t import surfaces.(I could import just the MRI as “.nii” file.)
So, I installed Brainvisa and made T1 MRI Pipeline files.
But, I can’t find “.nii.gz” file on my folder, sample_ctf/Anatomy/BrainVisa.
Tutorial says that “If Brainstorm still doesn’t have a .nii.gz format in Import MRI window, you’ll have to gunzip this file first.”

Question 1,
Would you please show me where I can find the “this file” and how to unzip it?

Question2,
How can I import surface data of head, Lhemi and Rhemi.mesh files?

I always have the message of " MRI orientation was non-standard and had to be reoriented. Apply the same orientation to the surface?
Then the same error message come up whenever I push “YES” or “NO” as "Line113 error mne_read_surface(lin113) Bad magic number (6449518) in surface files"
I already replaced new mesh files which were created in the BrainVisa by myself instead of default Brainstorm mesh files on sample_ctf folder.

2

Hi Kikuko,

  • The files “.nii” and “.nii.gz” are MRI files, they can both be directly imported in Brainstorm using the menu “Import MRI”
  • The BrainVISA surfaces have an extension “.mesh”, use the “Import surfaces” menu to import them (don’t forget to change the file format in the import dialog window). You get error messages because the file format is not correct.

A general advice: before you jump to analyze your own files, please follow exactly step by step the online tutorials, using the tutorial data, from the beginning to the end. With this documentation, if you read everything very carefully, it’s almost impossible to get lost.

Please, get back to us if you don’t find your answers in the online documentation.

Cheers,
Francois

3

Hi, Francois,

Thank you for your advice.
I’ve just done to import surfaces.
I found I made mistakes choosing the file format.
But, I don’t find how to get the “.nii.gz” files.
Would you please show me how to do?

Best regards,
Kikuko

4

Depending or your local configuration, BrainVISA MRI files can be: .nii, .nii.gz or .dim/.ima

For the online brainstorm tutorial:
Download sample_ctf.zip, unzip it, select: sample_ctf/Anatomy/01.nii

For your own MRI volumes:
If you are running into trouble, please contact the BrainVISA developers: http://brainvisa.info/