Re: [Freesurfer] bert functional data set

Hi Doug,

Thanks for your help. I also have a question regarding registering multiple functional scans to the anatomical so that way I can overlay activation T maps generated from SPM and extract ROI information. This tutorial uses a motion correction template.nii file generated from FS-FAST, and am wondering if there is any output (e.g. the realignment parameters txt file) from SPM that can be used instead of a motion correction template file.

Thanks,

Vanessa Palzes Research Assistant Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155

-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, April 07, 2011 12:40 PM To: Palzes, Vanessa Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bert functional data set

That tutorial is out of date. Try using the multimodal below.

doug

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal

Palzes, Vanessa wrote:

Hi,

I'm trying to go through this tutorial:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AutomaticRegistratio

nSpm

I have already downloaded/unpacked the buckner_data-tutorial-subjs.tar.gz, and also set up the correct SUBJECTS_DIR as: setenv TUTORIAL_DATA /Applications/freesurfer/subjects cd $TUTORIAL_DATA/buckner_data/tutorial_subjs setenv SUBJECTS_DIR ${PWD}

But, when I try to run the following command, it tells me it cannot

find

bert-brf...

spmregister --s bert-brf --mov f001.img --reg register.dat

Any suggestions on how I can locate and use this tutorial data?

Vanessa Palzes Research Assistant Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155

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