Hi, Freesurfer experts
If you try to read one of the posterior*.mgz files generated by reco-all
-hippo-subfield into MatLab/Octave using MRIread.m it fails like this:
Ps=MRIread('posterior_left_subiculum.mgz')
WARNING: error reading MR params
Attempted to access mr_parms(1); index out of bounds because
numel(mr_parms)=0.
Error in MRIread (line 100)
tr = mr_parms(1);
That is because the posterior*.mgz files does not have this data. I made
a creating a little customized nMRIread.m with the following
changes:
if numel(mr_parms) > 0
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
else
mr_parms(1) = 0;
mr_parms(2) = 0;
mr_parms(3) = 0;
mr_parms(4) = 0;
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
end
That works but it is only a quick workaround since MRIread,m calls
load_mgh.m and it shows a warning message about the mr_parms. This
message does not block my work but it is not good to see the warning all
the time on my screen. Perhaps the best fix would be just creating the
posterior*.mgz files with these data defined as 0. But I would be happy
if I could just "edit" these files defining these values. Is there a
freesurfer tool to make this simple edition? I noticed, for example,
that when you use mri_concat to sum these files the resulting
concatenated file is fixed and these parameters are defined.
Thanks in advance,
Marcos.
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