Hi Vanessa, you have to use some sort of template volume. I'm not sure what SPM uses as the motion correction template. It's probably the middle time point or the average across all time points. But it is using something. You need to find out what it is and use that. doug
Palzes, Vanessa wrote:
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That tutorial is out of date.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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer