Hi Freesurfer experts,
We’ve been collecting structural (1mm isotropic) and functional (2.75x2.75x3mm) data on a Philips 3T scanner using an 8-channel head coil. We are reconstructing each subject’s surface and mapping functional data processed in FSL’s FEAT to the surface. For some subjects, we have only 1 MPRAGE, but for others, we have multiple (2 or 3) MPRAGEs, acquired in separate scanning sessions.
Looking back at the list serve and FSLwiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsQuizAnswers), it appears that our SNR should be good enough that we do not need -- and perhaps SHOULD NOT use --multiple MPRAGEs when using recon-all. Is there general agreement on this?
How does one go about quantitatively comparing one surface reconstruction derived from 1 MPRAGE to another derived from 2 MPRAGEs?
Thank you,
Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington
Hi Susan, if you are not doing a thickness study, then I don't think it will matter much if you have 1 or 2 or 3 T1s. There's not an easy way to compare the recons. You can do a paired difference using 1 T1 vs mult T1s. That will mostly give you bias information, not accuracy or repeatability. doug
On 07/30/2012 01:18 AM, Susan Alice McLaughlin wrote:
Hi Freesurfer experts,
We’ve been collecting structural (1mm isotropic) and functional (2.75x2.75x3mm) data on a Philips 3T scanner using an 8-channel head coil. We are reconstructing each subject’s surface and mapping functional data processed in FSL’s FEAT to the surface. For some subjects, we have only 1 MPRAGE, but for others, we have multiple (2 or 3) MPRAGEs, acquired in separate scanning sessions.
Looking back at the list serve and FSLwiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsQuizAnswers), it appears that our SNR should be good enough that we do not need -- and perhaps SHOULD NOT use --multiple MPRAGEs when using recon-all. Is there general agreement on this?
How does one go about quantitatively comparing one surface reconstruction derived from 1 MPRAGE to another derived from 2 MPRAGEs?
Thank you,
Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Susan
unfortunately there is no way to say which one is better except (a) visual inspection, and (b) comparison to previous results, which probably won't be terribly powerful. You can look at the reliability of the surfaces by comparing thickness in the N=1 and N=2 recons. With 8 channels I'm not sure, it depends a lot on coil geometry. We've had trouble with some 8 channel coils in the past due primarily to poor SNR near the top of the brain (the vertex)
cheers Bruce
On Sun, 29 Jul 2012, Susan Alice McLaughlin wrote:
Hi Freesurfer experts,
We?ve been collecting structural (1mm isotropic) and functional
(2.75x2.75x3mm) data on a Philips 3T scanner using an 8-channel head coil. We are reconstructing each subject?s surface and mapping functional data processed in FSL?s FEAT to the surface. For some subjects, we have only 1 MPRAGE, but for others, we have multiple (2 or 3) MPRAGEs, acquired in separate scanning sessions.
Looking back at the list serve and FSLwiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsQuizAnswers), it appears that our SNR should be good enough that we do not need -- and perhaps SHOULD NOT use --multiple MPRAGEs when using recon-all. Is there general agreement on this?
How does one go about quantitatively comparing one surface reconstruction derived from 1 MPRAGE to another derived from 2 MPRAGEs?
Thank you,
Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Susan Alice McLaughlin