Hi Inge,

if you just rerun recon-all with the orig as input it should work. It will skip the motion correction if you give it only a single volume.

cheers, Bruce

On Fri, 6 Jul 2007, Inge K. Amlien wrote:

Thanks, for the first study I converted the COR-files (residing in mri/orig/00*/) to mri/orig/001.mgz and 002.mgz and ran recon-all as normal.

For the second study, are the COR-files residing in folder mri/orig/COR-* equal to orig.mgz in 3.05? Is it ok to convert to mgz and run recon-all with -nomotioncor here, or has anything else been done to the data?

Have a nice day Inge

On Tue, July 3, 2007 17:56, Bruce Fischl wrote:

...

you should be able to use COR files as input On Tue, 3 Jul 2007, Inge K. Amlien wrote:

...

Hi, we are about to reprocess quite a few subjects originally done in 2004. I am wondering if I will need to dig up the original dicoms, or if I can convert the COR-files to .mgz.

-In the first study we have 2 series converted to orig/001/COR* and orig/002/COR*. -In the second study we have only 1 series, and only the orig/COR-files, (I believe the averaging step has been run somehow).

Does Freesurfer (3.05) handle the first steps any different now, or is okay to convert to .mgz and go from there?

Thanks, Inge

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