Hi Don

you don't need to convert the dicom series, just point recon-all at ONE file in the mprage series:

recon-all -i <full path and file name of one dicom file> \ -s <subject id> -sd <subject dir> -all

the list of labels is in $FREESURFER_HOME/FreeSurferColorLUT.txt, although it contains some labels for structures that we don't routinely segment (yet!). There are white matter labels in it as well.

cheers Bruce

On Tue, 29 Jul 2014, Krieger, Donald N. wrote:

I have an MPRAGE dicom file sequences on which I wish to run recon-all .

Here is the command I am using:

mri_convert DICOM_DIRECTORY SubjectName/mri/orig/001.mgz

It returns immediately with the error message:

corRead(): can’t open file DICOM_DIRECTORY/COR-.info

Your suggestions would be welcome.

Here are 2 other simple questions:

(1)    Where do I find the list of which labels correspond to which structures?

(2)    Are there labels for the white matter volumes or only for the gray matter volumes?  If they exist, where are they?

Regards,

Don