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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