cabeen / niftijio Goto Github PK

Hi @cabeen
I hope you are well, I got an error when I wanted to read a nifti file that had a .json extension. It may be my misunderstanding of the format.

 while (start_addr < (int) ds.vox_offset)
            {
                int[] size_code = new int[2];
                size_code[0] = di.readInt();
                size_code[1] = di.readInt();

                int nb = size_code[0] - NiftiHeader.EXT_KEY_SIZE;
                byte[] eblob = new byte[nb];
                di.readFully(eblob, 0, nb);
                ds.extension_blobs.add(eblob);
                ds.extensions_list.add(size_code);
                start_addr += (size_code[0]);
                if (start_addr > (int) ds.vox_offset)
                    throw new IOException("Error: Data  for extension " + (ds.extensions_list.size())
                            + " appears to overrun start of image data.");
            }

let's assume we have a JSON file (157 bytes) and 8 bytes for extension keys; when it reaches to end; the start_addr is 509, so It starts again and reads the first 8 bytes which may be wrong.
I think if it checks the size of the rest bytes, it could be solved. like this:

if(((int) ds.vox_offset - start_addr)<16)
                    break;

Kind regards,

Hi,
I was wondering if the niftijio could support nifti-2 or not?
Best,

Hi,
thank you very much for such a great library.
I want to use the dimension 5, 6, and 7. I understand it is not possible with this lib.
could I fork your repo and develop?
best,

Thanks for the great software!

Hi, I created a much improved version (in terms of efficiency) that uses a 1-d array (instead of 4-d) to store the data. Let me know if you want me to send it to you.

Jeremy

Hi Cabeen,

As already mentioned I think your library is very useful for the java medical imaging community.

It would be great if it could be published to Maven central, then we could simply add a dependency instead of having to clone to produce your own jar.
This would make it easily accessible to a wider audience. What do you think ?

Best,
Ghazi