[Neuroimaging] Loading dataset from directory to memory problem

[Ali khattak]

Hello respected all mailing community

I am glad to ask question here in such a responsive environment [image:
:blush:]
I am working on *CNN based detection and classification of Alzheimer
disease using MRI and Clinical data*
For that I am using ADNI dataset where all the nifty MRI scans are not same
shape. But the size of maximum number of files are (256,256,166).

I collected data from ADNI website and I cleaned it and splitted into
testing and training folder manually with their respective classes for
training my modal in future.
The data size is almost *17 GB*

Now my task is to load and visualize all those .nii files from directory to
the memory and convert them into *tensor torch* or *numpy array*. Both will
be applicable in my case
I am following data loading topics and already asked two question for data
loading to my memory.

I tried a lot my all tries find for exploring my problem here in Github My
Github Files <https://github.com/Aliktk/Code-for-AD-Dataloading->. It
contains what I did in last two months but I still didn’t get the right
direction.
I think here in this forum someone worked on 3D datasets like ADNI, OSIS etc.
need help for solving dataloading problem and many question about
dataloading.

*Question are:*

1-

Loading 3D or 4D data in pytorch in not a big deal as they have strong
libraries for computing this data. Beside dataloading tutorials anyone have
such kinds of methods or code which load 3D data without any preprocessing
and augmentation or subsampling??

1-

Is it important to convert each MRI file into patches for feed into my
memory and further processing?

2-

What is the best to subsample my MRI files?

3-

Loading MRI files need preprocessing?

4-

Does slicing make my work easy?

My data dimension are 256, 256, 166 and it may varying for some images and
the these files are in nii file format.

*Note:*

someone share his experiences but he is disappear from last week for
loading such data I simply do *typically do is create a list of direct
paths to the patient directories and then in the get_item method, I will
index this list and directly read and convert the nifti to a torch Tensor*.

but it didn’t work for me or i don’t know the code or something else but I
failed to load the data in such way.[image: :disappointed:]. *So I am
requesting with much respect that please help me someone in step by step
way please*

I have many question but the problem is that here in my institute no one
sharing and explaining these things. everyone says that you have to solve
by your own knowledge and google any problem. But I couldn’t find way to
figure out my problem

*Experts and my field related please help me* [image: :pray:]
*Ali Nawaz*
*Software Engineer*
*Research Assistant *
*University of Engineering and Technology Taxila, Pakistan*
*Cell Phone & Whatsapp: 03358043653*
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