Hello,
I have two questions.
1> I am following instructions from http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-platform-release...
Under GETTING STARTED WITH YOUR OWN DATA
there are two directives:
cp -r <path_to_dicoms>/95555-2-*.dcm 001/ cp -r <path_to_dicoms>/95555-3-*.dcm 002/
with special note: . Note that in your own case, the name of the dicom files will be different (in this example, 95555-2-*.dcm consisted of 128 files).
My MRI data is essentially a directory (directory name is a many digit number like 123456789) with four subdirectories named 1, 2, 3 and 4.
So I have used the following commands cp -r <path_to_dicoms>/12345..../1/*.dcm 001/ cp -r <path_to_dicoms>/12345.../2/.dcm 002/
This is because directories 2 and 3 have 256 slices whereas 1 and 4 had six slices. (this could change from subject to subject)
After that I do mri_convert -it dicom -ot mgz 001/ 001.mgz mri_convert -it dicom -ot mgz 002/ 002.mgz
Is this correct procedure? This does create the .mgz files.
2> After this, I gave the command
recon-all -autorecon-all -subjid <subjid>
and this has been running for many hours now (as warned on the website). It has already created slices and sets. My understanding is it will do just about everything INCLUDING triangulation which is used for BEM forward moderls using MNE. Is this correct?
Thanks for your help.
best, sameer