Hi Luca,
Welcome to the neuroimaging world.
Answers below
Pieter Vandemaele, MSc-Ing
GIfMI Site Manager
Ghent Institute for Functional and Metabolic Imaging
MR Department -1K12
Ghent University Hospital
De Pintelaan 185
9000 Ghent - BELGIUM
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tel: +32 (0)9 332 48 20
http://gifmi.ugent.be
fax: +32 (0)9 332 49 69
ORCID ID
0000-0002-4523-2476
-----Oorspronkelijk bericht-----
Van: SPM (Statistical Parametric Mapping) <[log in to unmask]> Namens Luca Cuffaro
Verzonden: dinsdag 18 februari 2020 13:28
Aan: [log in to unmask]
Onderwerp: [SPM] FIRST STEP (dicom to nii)
Dear all,
I am a neurologist (almost, last year trainee) and this is my first time I am working with MRI.
I have collected and worked with EEG recorded from stroke patients, but now I would like to normalise their brain MRI in order to mask the lesion and perform precise signal EEG analysis. I have just routine MRI collected in .dcom format, without any subfolders as T1, T2, DWI, etc.
I have read many manuals and listened to many tutorials, I have tried, but I am unable to find this basic, but fundamental information:
1. How can I organize an MRI dataset based on a list of .dcom files?
The best way is to use a validated converter and make conversion to BIDS (https://bids.neuroimaging.io/)
There are some converters available eg https://pypi.org/project/bidscoin/
2. How can I understand which .nii file I have to use in order to get a correct images?
This question is a bit unclear
3. Do I need to do something in particular to blend axial, sagittal and coronal?
What do you mean with blend? Data is stored in a 3D matrix in NIfTI. Viewers resample on the fly the 3D matrix to show the requested images.
I perfectly know that it is a very basic and for most of you stupid message, but I don't know how to go forward.
Any help or suggestions are being to be super accepted.
Thanks,
Luca
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