Hey guys,
I sent one messge before but it was very vague, but now that I am a little bit more knowledgeable about what I am doing, let me be more specific. I have a bunch of images (individual slices) in .dcm format. What EXACTLY should I type in the command line to convert these to .cor files? I've been fiddling with the mri_convert command, and I thought it worked at first, but the files themselves didn't say .cor after I was finished with the "conversion." Also, should I FIRST move the files into an orig directory that I have created, THEN convert them, visa versa, or does it not matter what order I do that in? When I convert the files, I dont know how to convert ALL of the slices in the folder, but I was rather trying to individually convert the files at first, which would take forever. I have gotten several errors wheile trying to convert, but mostly I get ones having to do with the output I am putting into the command.
One more thing. Suppose this converion/moving the files works...I am confused as to why you need to make subdirectories under the orig directory labled 001 002 003. Are there more than just 3 I am supposed to make, and what exactly do I put in these subcategories?
Once I get over this road block I should be alright because I was able to do everything properly with the bert file. Thanks.
Dave
Hi Dave,
you make subdirs if you have more than one acquisition of the same subject that you want to motion correct and average. It's a good idea to keep the dicom files in an orig/dicom dir so you can always get back to them. If that's the case, pick 1 file from the dicom series that you want to convert and run (from the subject's mri dir):
mri_convert orig/dicom/<one file>.dcm orig
or if you have multiple runs, but them in orig/001 etc... This will create a bunch of COR-* files.
cheers, Bruce
On Tue, 28 Jun 2005, David Soscia wrote:
Hey guys,
I sent one messge before but it was very vague, but now that I am a little bit more knowledgeable about what I am doing, let me be more specific. I have a bunch of images (individual slices) in .dcm format. What EXACTLY should I type in the command line to convert these to .cor files? I've been fiddling with the mri_convert command, and I thought it worked at first, but the files themselves didn't say .cor after I was finished with the "conversion." Also, should I FIRST move the files into an orig directory that I have created, THEN convert them, visa versa, or does it not matter what order I do that in? When I convert the files, I dont know how to convert ALL of the slices in the folder, but I was rather trying to individually convert the files at first, which would take forever. I have gotten several errors wheile trying to convert, but mostly I get ones having to do with the output I am putting into the command.
One more thing. Suppose this converion/moving the files works...I am confused as to why you need to make subdirectories under the orig directory labled 001 002 003. Are there more than just 3 I am supposed to make, and what exactly do I put in these subcategories?
Once I get over this road block I should be alright because I was able to do everything properly with the bert file. Thanks.
Dave _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
David Soscia