Hi, Doug
Hi, all
This single BASH script line works like a charm for all posterior.mgz
files in a once and keeps the original names (must be in yoursubject/mri
folder).
for f in $(ls posterior*.mgz); do mri_convert -tr 0 -ti 0 -te 0
-flip_angle 0 -i $f -o $f; done
You can also use in a more complete script like:
#!/bin/bash
#usage myrecon subj (for example, myrecon bert)
mkdir ~/freesurfer/subjects/$1/mri/orig -p
cp ~/freesurfer/ImgOrig/$1/* ~/freesurfer/subjects/$1/mri/orig/
recon-all -all -s $1 -cw256 -hippo-subfields -qcache
cd ~/freesurfer/subjects/$1/mri
for f in $(ls posterior*.mgz); do mri_convert -tr 0 -ti 0 -te 0
-flip_angle 0 -i $f -o $f; done
This way all files will be fixed just after usual recon-all pipeline.
Notice you may adapt for your environment and recon-all options. Also,
ImgOrig is a custom folder where I have 1 folder for each of my subjects
with their respective images already prepared as 00x.mgz.
I hope you think it is useful.
BTW, I had to specify -i and -o in the command line. Using just the name
of the files did not work.
Thank you again, Doug.
Marcos
Em Ter, 2013-06-18 às 23:45 -0700, Douglas Greve escreveu:
> 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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> > Freesurfer@nmr.mgh.harvard.edu
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>
>
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