Hi Ilana

The double slashes shouldn't matter. What does it say when you give

tkmedit bert brainmask.mgz

in the freesurfer environment ( i.e. after you run SetUpFreeSurfer.csh )

Krish

On 12/14/09 5:27 PM, Ilana Hairston wrote:

Hi there, I moved my data to a new computer with Freesurfer installed. When i run the SetUpFreeSurfer.csh (or .sh for that matter) i get a strange configuration:

Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/ FSFAST_HOME /usr/local/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer//subjects MNI_DIR /usr/local/freesurfer//mni FSL_DIR /usr/local/fsl

note the double slashes on SUBJECTS_DIR, FSFAST_DIR, and MNI_DIR.

needless to say freesurfer can't find my data.

I inspected the setup files and they don't have typo in them.

what should i do?

thanks ilana

--

---

Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449

---

Sentimental Insomnia and Nostalgia Disorders Sciences

---

---

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