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Miriam Schwalm
Apr 16, 2019, 1:43:01 PM4/16/19
to mvpa-t...@googlegroups.com, mvpa_s...@princeton.edu
Dear mvpa-toolbox team,
we are currently exploring your functions write_to_afni.m and zeroify_write_afni.m as we want to write out a matrix from Matlab (reconstructed from BRUKER's 2dseq file) into a .BRIK and .HEAD to subsequently analyse the data in AFNI (the idea is to circumvent the use of heavy dicom files).
From https://github.com/PrincetonUniversity/princeton-mvpa-toolbox/wiki/HowtosExporting#exporting I got the idea that I could use zeroify_write_afni.m and feed it with my previously constructed volume data matrix (x, y, z, t) and the filenames for the BRIK/HEAD pair which are used as templates in the function.
What still is unclear to me is how I could get/make a sample BRIK/HEAD pair of the right resolution and orientation which would be usable and how I could verify that it indeed has the resolution and orientation needed for my data (i.e. is it different for 2D and 3D sequences, etc.)?
I have Ziad Saad's toolbox which includes the WriteBrik function needed for zeroify_write_afni.m to run and also have his Demo Bricks folder but I am not sure how to proceed from here.
Any comment or advice is highly appreciated, thank you very much in advance!
Best,
Miriam
Greg Detre
Apr 28, 2019, 5:31:54 AM4/28/19
to mvpa-t...@googlegroups.com, mvpa_s...@princeton.edu
Hi Miriam,
It's been a while since I tried this, but here's my best recollection: the idea was to take a BRIK file that you already have from the scanner of the right parameters, and use that as the template. The reason for doing it this way is that it's hard to generate a BRIK file from scratch that's fully correct...
g
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