Have you tried dcm2niix? It's pretty robust
On 6/17/2021 6:59 PM, Christopher Mcnorgan wrote:
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Hi all,
I’ve been provided with some data collected on a 1.5T GE scanner from an old published study. The paper doesn’t indicate the scanner model (beyond that it’s a 1.5 GE scanner), but I believe they came from a GE Genesis, based on the .MR file extension. I have successfully used MRIcro to convert the series of .MR files from the anatomical scan to Analyze format, so there’s nothing wrong with the files.
I would prefer to script mri_convert to convert the data, but I am having problems doing so, as each of my attempts results in a segmentation fault. Files were originally named <pattern>1.MR to <pattern>128.MR, and based on the program output prior to the core dump, I renamed them so that the file numbers were zero-padded, and I’ve tried it with and without the input filetype argument, but I get the segmentation fault/core dump either way. The command I’m trying is:
mri_convert -i E11816S5I001.MR -it ge -o T1.nii.gz
This gives me:
reading from E11816S5I001.MR...
fname_format : /home/fruit/music/tmp/E11816/mri/S5/renumbered/E11816S5I%d.MR
fname_format2 : /home/fruit/music/tmp/E11816/mri/S5/renumbered/E11816S5I%03d.MR
Segmentation fault (core dumped)
I was hoping someone could point out something that I’m missing.
Thanks for your time. It’s much appreciated.
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Chris McNorgan
Assistant Professor
Department of Psychology
University at Buffalo,
The State University of New York
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