[MINC-users] negative zstep causes trouble

[Marc Schoenwiesner]

Hi,

I am struggling with the conversion/analysis of fMRI data from outside
BIC, but have located the problem more or less. Maybe someone knows about this.

Problem: fmr_preprocess crashes with a dynamic minc file.
The trouble maker is the positive zstep:
>>
file: run1.mncimage: signed__ short 0 to 4095
image dimensions: time zspace yspace xspace dimension name
length step start
    --------------         ------         ----        -----
    time                       71            9            0
    zspace                     19            4     -3.29857
    yspace                     64     -3.12497      95.4729
    xspace                     64     -3.12497      97.9577
>>

fmr_preprocess crashed when resampling the volume, because $nelem_z (resampling
steps in z direction) gets negative. I copied fmr_preprocess and added an abs()
to the 238 to make the calculation robust against positive zsteps:
    $nelem_z = abs (int ((($z_sp - 1) * $z_step ) / $resampling_step));

This step works now. The next hang is when minctracc is called. I found that
this is because the center of gravity of the volume seems to be either
incorrectly calculated by volume_cog, or minctracc cannot handle centroids in
certain quadrants.

center with zstep=4   0.912580 -4.248807  35.571903 (minctracc crashes)
center with zstep=-4 -0.077238 -9.411657 -41.277493 (works fine)

I can work around this problem by setting zstep to -4:
% minc_modify_header -dinsert zspace:step=4 run1.mnc
then run fmr_preprocess and setting it back, but this is ugly and I might mess
up my file orientations (this is a left-brain right-brain thing, so I really
don't want to risk anything of that sort. By the way, mincreshape +/-zdirection
doesn't seem to do anything at all with this file.)

volume_cog and mictracc are binary, so I am stuck here.
I'd be very grateful if anyone could clarify the centroid issue! I am new to the
BIC and MINC (had my first look at the software this week) and don't seem to be
able to get this straightened out myself.

Cheers
Marc