All those commands will do the same thing. When you pass mri_convert a single dicom file, it looks at all the files in that directory and finds all the dicoms that have the same series number, and puts them into one volume.

Alexa Nardelli wrote:

Hi,

I have a question regarding converting files to mgz format from siemens (dicom). Per each image I have 144 IMA files (i.e. for one subject I have files from .001.IMA to .144.IMA) and I am wondering how to convert those into 1 mgz file. The only way I seem to find is to use the command:

mri_convert filename.001.ima subjectname/mri/orig/001.mgz

mri_convert filename.002.ima subjectname/mri/orig/002.mgz

...

mri_convert filename.144.ima subjectname/mri/orig/144.mgz

While this is painful and time consuming I also worry that in my quest to find the hippocampal volumes, Freesurfer will not read these files as one volume.

Is this the correct way to convert these files? Or is there another easier way?

Thanks

Alexa _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer