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That tutorial is out of date.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

Hi Vanessa, you should register each run separately. After that you can sample them on the surface (mri_vol2surf), at which point they will be in registration (so you can average them together). Alternatively, you can map the anatomical ROIs back into the functional space of each run with mri_label2vol.

doug

On 4/13/11 8:20 PM, Palzes, Vanessa wrote:

Hi Doug,

I determined that SPM does create a mean volume during motion correction. My question now is how do I incorporate several functional runs (each with a different "template" mean volume from motion correction) into a registration with the anatomical. I have statistical activation maps generated based on 4 functional runs, so eventually I would like to overlay this on the anatomical volume in Freesurfer and extract information from ROIs. If I were to use one of the "template" mean volumes (say from function run 1) to conduct the registration then I would be assuming that the subject did not move across the rest of the runs.

Your thoughts are greatly appreciated.

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: Wednesday, April 13, 2011 1:12 PM To: Palzes, Vanessa Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bert functional data set

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