Hi Sahin,
On Oct 5, 2010, at 10:07 , Shahin wrote:
Hi,
I have received a dataset of high resolution monkey structural scans (0.5 mm * 0.5mm * 0.5mm) collected by GE machines. Now I have two problems that I appreciate if you help me with them,1- mri_convert can not convert these files to mgh format and I don't now why. Error message says that they are not dicom while even the linux machine detects them as dicom.
No idea, I am on a Siemens.
2- How can I reduce the resolution to 1mm rather than 0.5 to further use them with freesurfer?
# the first one keeps the initial bit resolution mri_convert -i ${src_dir}/${src_file_name} -o ${targ_dir}/${highres_conformed_vol} -iis 1 -ijs 1 -iks 1 --conform --no_scale 1 -nc # this one rescales to 8bit mri_convert -i ${src_dir}/${src_file_name} -o ${targ_dir}/${conformed_vol} -iis 1 -ijs 1 -iks 1 --conform
the required conversion sits in "-iis 1 -ijs 1 -iks 1" here you give the resolution that will end up in the header without changing the data. If you are interested I have a bunch of scripts for processing monkeys (that still need loads of manual intervention) I am williong to share.
Best Sebastian
I have attached one of those dicom files to this e-mail. Apparently their name format is also very different from ours.
Best Regards
Shahin Nasr
PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
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