External Email - Use Caution        

Dear Doug

Just to be clear

I  ran the 1st process on subject x with

recon-all -s x -T2 volT2.nii  -T2pial 

It still needed wm edits. On rerun, can I just do

 

recon-all -s x  autorecon2-wm -autorecon3

or I need to reuse the T2 for best results

recon-all -s x  autorecon2-wm -autorecon3  -T2 volT2.nii  -T2pial   

If so, can I obtain similar results with mri/orig/T2 raw.mgz instead of the volT2.nii input?

Thanks, 

OL

On Mon, May 4, 2020 at 10:49 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Sorry, our interface is a little bit confusing on this. Use -T2 to specify the T2 volume (eg, -T2 /path/to/T2.mgz). To apply the T2 to the pial use -T2pial (without any arguments)

On 5/2/2020 7:55 PM, Octavian Lie wrote:

        External Email - Use Caution        

Dear All, 

I ran recon-all on the 1st run using the -T2pial flag. After wm.mgz edits, when running

recon-all autorecon2-wm -autorecon3 -T2pial volT2.mgz

it throws an error ~ 'flag volT2.mgz not recognized'. When reruning recon-all as above, do we need to include the T2pial flag to make use of the t2 pial information? If not, is the previous T2pial output used to regenerate the pia?

Thank you, 

OL

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

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

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