Hi all
I have collected some raw Arterial Spin Labeling (ASL) data. I would like to use freesurfer to create perfusion maps of this data. Is it possible to take the raw data, motion correct it, perform a pairwise subtraction, and then average all the subtractions to create a mean perfusion map? Please let me know if you have ideas on how to do this sort of thing.
Thanks Abi
We don't have an MC program. You can try running FSL's FLIRT or AFNI's 3dvolreg. As for analysis, you should be able run
mri_concat --paired-diff --mean inputaslvolume outputvolume
I've never actually tried it like this, but it should work.
doug
On Mon, 27 Nov 2006, Abi Gopal wrote:
Hi all
I have collected some raw Arterial Spin Labeling (ASL) data. I would like to use freesurfer to create perfusion maps of this data. Is it possible to take the raw data, motion correct it, perform a pairwise subtraction, and then average all the subtractions to create a mean perfusion map? Please let me know if you have ideas on how to do this sort of thing.
Thanks Abi
Indeed - you don't just want to do pairwise subtraction Abi, it's better to do sub-TR timing-adjustment on the tagged and control data before subtraction - if you look in the latest version of FEAT in FSL you'll see options for easy preprocessing of ASL data. You would then be able to use the normal methods for transferring FEAT data into FreeSurferSpace.
Cheers, Steve.
On 27 Nov 2006, at 17:47, Doug Greve wrote:
We don't have an MC program. You can try running FSL's FLIRT or AFNI's 3dvolreg. As for analysis, you should be able run
mri_concat --paired-diff --mean inputaslvolume outputvolume
I've never actually tried it like this, but it should work.
doug
On Mon, 27 Nov 2006, Abi Gopal wrote:
Hi all
I have collected some raw Arterial Spin Labeling (ASL) data. I would like to use freesurfer to create perfusion maps of this data. Is it possible to take the raw data, motion correct it, perform a pairwise subtraction, and then average all the subtractions to create a mean perfusion map? Please let me know if you have ideas on how to do this sort of thing.
Thanks Abi
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---
Hello all
I am still having some trouble getting started on preprocessing of my ASL data. Steve Smith has suggested that I do sub-TR timing-adjustment before a subtraction analysis in FEAT. I wonder if anyone in the Martinos center has expertise with this kind of analysis. If possible, I'd like to stop by the Martinos center for a short tutorial in preprocessing ASL data. If anyone there can help me with this, please let me know. I don't think it should take too long (30 min or less), and it would really help me out, as I am quite new to all of this software.
Thanks Abi
On 11/27/06, Steve Smith steve@fmrib.ox.ac.uk wrote:
Indeed - you don't just want to do pairwise subtraction Abi, it's better to do sub-TR timing-adjustment on the tagged and control data before subtraction - if you look in the latest version of FEAT in FSL you'll see options for easy preprocessing of ASL data. You would then be able to use the normal methods for transferring FEAT data into FreeSurferSpace.
Cheers, Steve.
On 27 Nov 2006, at 17:47, Doug Greve wrote:
We don't have an MC program. You can try running FSL's FLIRT or AFNI's 3dvolreg. As for analysis, you should be able run
mri_concat --paired-diff --mean inputaslvolume outputvolume
I've never actually tried it like this, but it should work.
doug
On Mon, 27 Nov 2006, Abi Gopal wrote:
Hi all
I have collected some raw Arterial Spin Labeling (ASL) data. I would like to use freesurfer to create perfusion maps of this data. Is it possible to take the raw data, motion correct it, perform a pairwise subtraction, and then average all the subtractions to create a mean perfusion map? Please let me know if you have ideas on how to do this sort of thing.
Thanks Abi
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve
freesurfer@nmr.mgh.harvard.edu
-
Abi Gopal -
Doug Greve -
Steve Smith