Hello,
Josh Roffman and I recently ran an fMRI scan. Our subject's data viewed in tkmedit seemed to be shifted inferiorly in the coronal view by a wide margin (an inch or so), leaving no functional activation in the top of the cortex, even when set at an extremely low threshold.
When running the fMRI scan, we checked our slice prescription and ensured the area of view covered the entire cortex. We also checked the raw data output during the scan in the viewing window, and functional activity was present.
After running the unpacking and recon-all processes, I ran the pre-proc command and spm-register, and viewed the output using tkregister2. The registered functional data matched up beautifully with the underlying anatomy, and went right to the top of the cortex in the coronal view.
We ran our analysis using the appropriate paradigm files (has worked without fail for our previous subjects) and there is no functional activity in the top inch or so of the cortex whatsoever.
Please let me know if you have an answer to how this could have happened.
Dave Brohawn
Hi Dave, I'm not sure where to begin with this. Can you give more info? In particular, you might look at surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for ways to report issues efficiently.
doug
Dave Brohawn wrote:
Hello,
Josh Roffman and I recently ran an fMRI scan. Our subject's data viewed in tkmedit seemed to be shifted inferiorly in the coronal view by a wide margin (an inch or so), leaving no functional activation in the top of the cortex, even when set at an extremely low threshold.
When running the fMRI scan, we checked our slice prescription and ensured the area of view covered the entire cortex. We also checked the raw data output during the scan in the viewing window, and functional activity was present.
After running the unpacking and recon-all processes, I ran the pre-proc command and spm-register, and viewed the output using tkregister2. The registered functional data matched up beautifully with the underlying anatomy, and went right to the top of the cortex in the coronal view.
We ran our analysis using the appropriate paradigm files (has worked without fail for our previous subjects) and there is no functional activity in the top inch or so of the cortex whatsoever.
Please let me know if you have an answer to how this could have happened.
Dave Brohawn _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry for asking same question here again. I asked Dung before holiday about the criteria of good registration of fMRI and thickness map. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08913.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08913.html I paste my question again: what is the best registration of example_func and orig.mgz? In another word, what should I check besides things in the FS tutorial when I check/modify the registration in tkregister2? Is there golden reference points I can use?
I will appreciate if Dave could give more explanation or references of "beautiful match between functional and structural images".
Thank you in advance.
Xin Wang
________________________________
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 2:03 PM To: Dave Brohawn Cc: jroffman@partners.org; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem with post-spm registered data
Hi Dave, I'm not sure where to begin with this. Can you give more info? In particular, you might look at surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for ways to report issues efficiently.
doug
Dave Brohawn wrote:
Hello,
Josh Roffman and I recently ran an fMRI scan. Our subject's data viewed in tkmedit seemed to be shifted inferiorly in the coronal view by a wide margin (an inch or so), leaving no functional activation in the top of the cortex, even when set at an extremely low threshold.
When running the fMRI scan, we checked our slice prescription and ensured the area of view covered the entire cortex. We also checked the raw data output during the scan in the viewing window, and functional activity was present.
After running the unpacking and recon-all processes, I ran the pre-proc command and spm-register, and viewed the output using tkregister2. The registered functional data matched up beautifully with the underlying anatomy, and went right to the top of the cortex in the coronal view.
We ran our analysis using the appropriate paradigm files (has worked without fail for our previous subjects) and there is no functional activity in the top inch or so of the cortex whatsoever.
Please let me know if you have an answer to how this could have happened.
Dave Brohawn _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
There is no gold standard. Mainly just visualizing it with the surfaces and making sure the surfaces line up with the bright and dark folds in the EPI, as it says in the tutorial.
doug
Wang, Xin wrote:
Sorry for asking same question here again. I asked Dung before holiday about the criteria of good registration of fMRI and thickness map. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08913.html I paste my question again: what is the best registration of example_func and orig.mgz? In another word, what should I check besides things in the FS tutorial when I check/modify the registration in tkregister2? Is there golden reference points I can use?
I will appreciate if Dave could give more explanation or references of "beautiful match between functional and structural images".
Thank you in advance.
Xin Wang
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 2:03 PM To: Dave Brohawn Cc: jroffman@partners.org; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem with post-spm registered data
Hi Dave, I'm not sure where to begin with this. Can you give more info? In particular, you might look at surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for ways to report issues efficiently.
doug
Dave Brohawn wrote:
Hello,
Josh Roffman and I recently ran an fMRI scan. Our subject's data
viewed in
tkmedit seemed to be shifted inferiorly in the coronal view by a wide margin (an inch or so), leaving no functional activation in the top
of the
cortex, even when set at an extremely low threshold.
When running the fMRI scan, we checked our slice prescription and ensured the area of view covered the entire cortex. We also checked the raw data output during the scan in the viewing window, and functional activity was present.
After running the unpacking and recon-all processes, I ran the pre-proc command and spm-register, and viewed the output using tkregister2. The registered functional data matched up beautifully with the underlying anatomy, and went right to the top of the cortex in the coronal view.
We ran our analysis using the appropriate paradigm files (has worked without fail for our previous subjects) and there is no functional activity in the top inch or so of the cortex whatsoever.
Please let me know if you have an answer to how this could have happened.
Dave Brohawn _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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@nmr.mgh.harvard.edu
-
Dave Brohawn -
Doug Greve -
Wang, Xin