Hi Marcos, it is weird that the posterior*.mgz does not have that info.
Maybe Koen or Eugenio know why. In the mean time, you can use
mri_convert to change/set the parameters, eg
mri_convert in.mgz out.mgz -tr 0 -ti 0 -te 0 -flip_angle 0
doug
On 6/18/13 2:50 PM, Marcos Martins da Silva wrote:
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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