We are trying to work through a set of data with freesurfer but find that we are
stuck at the initial step of conversion. I am certain that there is something
small we are missing, and would appreciate any suggestions.
Our input images are raw from our 1.5 T GE LX system and we want to rewrite them
as COR .
We set up the directories mri/orig within orig we have 3 dirs each containing a
124 slice spgr: 001 002 003
Running mri_convert from the command line in the mri directory, we have tried:
1. mri_convert 001/I.001 as per the tutorial, but it wants an output file name
2. mri_convert 001/I.001 data1
but it wants an output format
after looking at the various options we tried:
3. mri_convert -ot cor 001/I.001 data1
it runs but is not actualy doing the conversion
Also, when I tried this from the gui it does not obtain the header info., which
I am guessing is diagnostic.
When the data comes off our scanner there is a header included in the main
directory (e.g.,SHDR.05192) that refers to the exam.
There is also a header in the anatomical series directory, in this case "002"
(e.g., SERHDR.002)
Thanks in advance for any help.
