Hello everyone,
I'm having trouble running mri_convert on the dicom images
coming off our Siemens Allegra 3T head-only scanner.
With this command line:
> mri_convert 5308.dcm
> /Volumes/Storage/data/freesurfer/subjects/scfr/mri/orig/001.mgz
I get this error:
> unknown file type for file 5308.dcm
Setting the input type to Siemens:
> mri_convert -it siemens 5308.dcm
> /Volumes/Storage/data/freesurfer/subjects/scfr/mri/orig/001.mgz
I get this error:
> reading from 5308.dcm...
> ERROR: could not parse
> /Volumes/Storage/data/freesurfer/subjects/scfr/mri/orig/01/5308.dcm
> ERROR: siemensRead():
> /Volumes/Storage/data/freesurfer/subjects/scfr/mri/orig/01/5308.dcm
And trying the siemens_dicom format (that perhaps I should have started with,
in the first place):
> mri_convert -it siemens_dicom 5308.dcm
> /Volumes/Storage/data/freesurfer/subjects/scfr/mri/orig/001.mgz
I get:
> reading from 5308.dcm...
> ERROR: /Volumes/Storage/data/freesurfer/subjects/scfr/mri/orig/01/5308.dcm is
> not a siemens DICOM file
> INFO: loading series header info.
Followed by a series of malloc errors similar to this one:
> mri_convert(5315) malloc: *** Deallocation of a pointer not malloced:
> 0x3fc7; This could be a double free(), or free() called with the middle of an
> allocated block; Try setting environment variable MallocHelp to see tools to
> help debug
followed by a Bus error.
What am I doing wrong? We are now running Tiger (10.4.2) on our G5.
I stuck a copy of the first image in the series here:
http://freylab.uoregon.edu/freesurfer/5308.dcm
Please let me know if this input format is not supported, yet, or
what additional information I can provide to help solve this problem.
I can probably come up with a work-around, like going through NIfTI
format, if necessary, but it would be neat to be able to skip the
additional step and import the .dcm files directly into FreeSurfer.
Thanks for your help or advice,
Colleen Tuffy
Human Neuroimaging Lab
University of Oregon
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