I've two questions regarding hippocampal subfield segmentation:
1, Is there any article or other document which containes an optimal T2 protocol with detailed sequence parameters for hippocampal subfield segmentation? (eg. BW, echo time, repetition time, FOV, echo train, paralell imaging on/off, ...) We have a Siemens Prisma 3T scanner.
2, For T1, we use the suggested MPRAGE protocol by Andre (1mm*1mm*1mm). Is it OK or do we need a special protocol?
Thank you, Gabor
Hi Gabor, A good place to start is ADNI’s high-res hippocampal T2 protocol. You can find the details on their website. It’s a coronal, anisotropic acquisition of a slab covering the hippocampus (0.4mm in plane, 2mm thickness, 25-30 slices). I’ve been playing a bit with more isotropic acquisition myself, but haven’t drawn any conclusions yet. Cheers, /Eugenio PS: 1mm MPRAGE is good.
-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Gabor Perlaki petzinger.gabor@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, 4 December 2017 at 10:20 To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] MRI protocol for hippocampal subfield segmentation
I've two questions regarding hippocampal subfield segmentation:
1, Is there any article or other document which containes an optimal T2 protocol with detailed sequence parameters for hippocampal subfield segmentation? (eg. BW, echo time, repetition time, FOV, echo train, paralell imaging on/off, ...) We have a Siemens Prisma 3T scanner. 2, For T1, we use the suggested MPRAGE protocol by Andre (1mm*1mm*1mm). Is it OK or do we need a special protocol? Thank you, Gabor
Dear Eugenio,
The ADNI protocol is quite similar to the default Siemens highres hippocampus protocol, however I haven't find a more detailed version of this one: http://adni.loni.usc.edu/wp-content/uploads/2017/07/ADNI3- MRI-protocols.pdf Do you know a more detailed version of the ADNI protocol?
In the default Siemens highres hippocampus T2 protocol the 2D distortion correction is turned on, while the distortion correction is turned off in both the default T1 MPRAGE Siemens morphometry protocol and the 1*1*1mm^3 T1 MPRAGE protocol suggested by Andre. Is it problem for hippocampal subfield segmentation if I use distortion corrected highresolution T2 TSE and uncorrected T1 MPRAGE images for the evaluation?
Thank you in advance, Gabor
2017-12-04 11:19 GMT+01:00 Gabor Perlaki petzinger.gabor@gmail.com:
I've two questions regarding hippocampal subfield segmentation:
1, Is there any article or other document which containes an optimal T2 protocol with detailed sequence parameters for hippocampal subfield segmentation? (eg. BW, echo time, repetition time, FOV, echo train, paralell imaging on/off, ...) We have a Siemens Prisma 3T scanner.
2, For T1, we use the suggested MPRAGE protocol by Andre (1mm*1mm*1mm). Is it OK or do we need a special protocol?
Thank you, Gabor
Hi again, You can find the detailed protocols here: http://adni.loni.usc.edu/methods/documents/mri-protocols/ Click on your scanner model (or similar) and search for the sequence “HighResHippcampus”. Regarding the distortion correction: I’ll leave this one for Andre ;-) Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Gabor Perlaki petzinger.gabor@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, 4 December 2017 at 16:05 To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation
Dear Eugenio, The ADNI protocol is quite similar to the default Siemens highres hippocampus protocol, however I haven't find a more detailed version of this one: http://adni.loni.usc.edu/wp-content/uploads/2017/07/ADNI3-MRI-protocols.pdf Do you know a more detailed version of the ADNI protocol?
In the default Siemens highres hippocampus T2 protocol the 2D distortion correction is turned on, while the distortion correction is turned off in both the default T1 MPRAGE Siemens morphometry protocol and the 1*1*1mm^3 T1 MPRAGE protocol suggested by Andre. Is it problem for hippocampal subfield segmentation if I use distortion corrected highresolution T2 TSE and uncorrected T1 MPRAGE images for the evaluation? Thank you in advance, Gabor
2017-12-04 11:19 GMT+01:00 Gabor Perlaki <petzinger.gabor@gmail.commailto:petzinger.gabor@gmail.com>: I've two questions regarding hippocampal subfield segmentation:
1, Is there any article or other document which containes an optimal T2 protocol with detailed sequence parameters for hippocampal subfield segmentation? (eg. BW, echo time, repetition time, FOV, echo train, paralell imaging on/off, ...) We have a Siemens Prisma 3T scanner. 2, For T1, we use the suggested MPRAGE protocol by Andre (1mm*1mm*1mm). Is it OK or do we need a special protocol? Thank you, Gabor
-- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-2084367 E-mail: petzinger.gabor@gmail.commailto:petzinger.gabor@gmail.com
freesurfer@nmr.mgh.harvard.edu
-
Gabor Perlaki -
Iglesias Gonzalez, Eugenio