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. 2- How can I reduce the resolution to 1mm rather than 0.5 to further use them with freesurfer?
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
Hello Freesurfer Users,
I am feeling very bad when I am using mri_convert. There are two problems: 1. When I converted a file in mgz format to nii.gz format, and did some volume calculation (mask and addition) by using fslmaths from FSL, then converted back to mgz. If the image type is uchar, it works fine. If the image type is int, the intensities changed. The 0¹ value is changed to 2.1e+09¹, others also in very large number (look like read the data from wrong place). Here is the code I used:
${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgz aparc+aseg.nii.gz -odt int ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add right_vect_mask aparc+aseg ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz -odt int
If no fslmaths calculation, convert back to mgz right way, no problem found.
2. when the conform is used, some head were rotated a little bit, but not for others. I am wondering how to avoid the rotation?
Regards, Wayne
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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Sebastian Moeller -
Shahin -
Wayne Su