Hi Freesurfers, We would like to optimize the 'Freesurferability' of images for a new project involving fidgety young children. Ideally, the structural scan time will be under 5 minutes. We have a GE Signa 3T MR750, with an 8-channel head coil. Preliminary experiments have found two short structural scan options, but both require some intervention after autorecon2 in the Freesurfer pipeline.
Does anyone have a suggestion for a sequence that
a) runs in under 5 minutes b) freesurfs with minimal intervention
and c) that they would be kind enough to share.
Thank you in advance, Mira ____________________________________________________ Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 94305 (650)498-4620
Dear Sira Using the same scanner we developed this sequence for Freesurfer analysis BRAVO: TR=9.2 ms; TE = 3.7 ms; flip angle 12°; FOV = 25.6 cm; preparation time= 650 ms; slice thickness= 1 mm; Bandwith= 25. Running time: 5 min, 32 sec.
---------------------------------------------------------------------- Antonio Cerasa, PhD Neuroimaging Research Unit, National Research Council, Catanzaro, 88100 Italy.
----- Original Message ----- From: "Mira Michelle Raman" mraman@stanford.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 16, 2010 7:27 PM Subject: [Freesurfer] Any suggestions for imaging parameters on a GE 3T with 8 channel head coil
Hi Freesurfers, We would like to optimize the 'Freesurferability' of images for a new project involving fidgety young children. Ideally, the structural scan time will be under 5 minutes. We have a GE Signa 3T MR750, with an 8-channel head coil. Preliminary experiments have found two short structural scan options, but both require some intervention after autorecon2 in the Freesurfer pipeline.
Does anyone have a suggestion for a sequence that
a) runs in under 5 minutes b) freesurfs with minimal intervention
and c) that they would be kind enough to share.
Thank you in advance, Mira ____________________________________________________ Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 94305 (650)498-4620
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that's an awfully short TR. Not sure how good the SNR is for the 8 channel, but that might be noisy. We also try to shorten the TE if we can, although you might not be able to. There is an ADNI mprage the exists on the GE platforms, although I'm not sure you're allowed to run it. It's a reasonable sequence. Your results will also depend on the geometry of the 8 coil elements. Some 8 channels we've seen have a very large signal falloff near the top of the head that make them difficult to analyze.
cheers Bruce
On Mon, 19 Jul 2010, antonio cerasa wrote:
Dear Sira Using the same scanner we developed this sequence for Freesurfer analysis BRAVO: TR=9.2 ms; TE = 3.7 ms; flip angle 12°; FOV = 25.6 cm; preparation time= 650 ms; slice thickness= 1 mm; Bandwith= 25. Running time: 5 min, 32 sec.
Antonio Cerasa, PhD Neuroimaging Research Unit, National Research Council, Catanzaro, 88100 Italy.
----- Original Message ----- From: "Mira Michelle Raman" mraman@stanford.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 16, 2010 7:27 PM Subject: [Freesurfer] Any suggestions for imaging parameters on a GE 3T with 8 channel head coil
Hi Freesurfers, We would like to optimize the 'Freesurferability' of images for a new project involving fidgety young children. Ideally, the structural scan time will be under 5 minutes. We have a GE Signa 3T MR750, with an 8-channel head coil. Preliminary experiments have found two short structural scan options, but both require some intervention after autorecon2 in the Freesurfer pipeline.
Does anyone have a suggestion for a sequence that
a) runs in under 5 minutes b) freesurfs with minimal intervention
and c) that they would be kind enough to share.
Thank you in advance, Mira ____________________________________________________ Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 94305 (650)498-4620
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello, Thank you both very much, I will definitely try these parameters next time I get development time on the scanner, and re-investigate the ADNI T1 sequence. Last time we tried it, I think the scans were on the order of 9 minutes, which just won't work with these particular participants. We definitely do have the 8-channel geometry issues Bruce mentioned and that was the main reason for my post, I had assumed that all the GE's with the 8-channel had the same problem we have been seeing, and we would love to be able to use FreeSurer without having to drop 100's or 1000's of control points for each subject, even after shortening the distance in N3 to 50.
Thank you both again, Sincerely, Mira
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "antonio cerasa" a.cerasa@isn.cnr.it Cc: "Mira Michelle Raman" mraman@stanford.edu, freesurfer@nmr.mgh.harvard.edu Sent: Monday, July 19, 2010 5:05:42 AM Subject: Re: [Freesurfer] Any suggestions for imaging parameters on a GE 3T with 8 channel head coil
that's an awfully short TR. Not sure how good the SNR is for the 8 channel, but that might be noisy. We also try to shorten the TE if we can, although you might not be able to. There is an ADNI mprage the exists on the GE platforms, although I'm not sure you're allowed to run it. It's a reasonable sequence. Your results will also depend on the geometry of the 8 coil elements. Some 8 channels we've seen have a very large signal falloff near the top of the head that make them difficult to analyze.
cheers Bruce
On Mon, 19 Jul 2010, antonio cerasa wrote:
Dear Sira Using the same scanner we developed this sequence for Freesurfer analysis BRAVO: TR=9.2 ms; TE = 3.7 ms; flip angle 12°; FOV = 25.6 cm; preparation time= 650 ms; slice thickness= 1 mm; Bandwith= 25. Running time: 5 min, 32 sec.
Antonio Cerasa, PhD Neuroimaging Research Unit, National Research Council, Catanzaro, 88100 Italy.
----- Original Message ----- From: "Mira Michelle Raman" mraman@stanford.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 16, 2010 7:27 PM Subject: [Freesurfer] Any suggestions for imaging parameters on a GE 3T with 8 channel head coil
Hi Freesurfers, We would like to optimize the 'Freesurferability' of images for a new project involving fidgety young children. Ideally, the structural scan time will be under 5 minutes. We have a GE Signa 3T MR750, with an 8-channel head coil. Preliminary experiments have found two short structural scan options, but both require some intervention after autorecon2 in the Freesurfer pipeline.
Does anyone have a suggestion for a sequence that
a) runs in under 5 minutes b) freesurfs with minimal intervention
and c) that they would be kind enough to share.
Thank you in advance, Mira ____________________________________________________ Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 94305 (650)498-4620
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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antonio cerasa -
Bruce Fischl -
Mira Michelle Raman