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Hi,

I try to answer but Eugenio may also add comments. Several points that are important:

- 1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm can manage.

- Post-aquisition reslicing to a higher resolution does not really increase the information content. Internally the algorithm works at a much higher resolution, anyway.

- If possible, switch to 3 Tesla.

- If possible and this is a prospective study, add a coronal T2 image and use the bi-channel option. See papers of Iglesias et al. on this.

- What you could also do on a 1.5 T is acquire the T1WI double and average it after coregistration, this increases the SNR.

- Generally, isometric resolutions are good due to the symmetry, of course.

- Also on 1.5 T, you may go bit below 1 mm with good head immobilization, and a longer scanning time. BRAVO in general is a good T1 option.

Best,

Philipp

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Ramesh Babu mgrameshbabu2013@gmail.com Gesendet: Freitag, 2. April 2021 09:29 An: Freesurfer support list; Umesh Rurdrapatna Betreff: Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

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Dear experts, Sorry for reposting. I am expecting some response from experts, so that I can proceed with confidence. For our project work, we are looking for hippocampal and its subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with 1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced images with a lot of noise. Then we tried the same sequence with 1x1x2 resolution, and 256x256x80 FOV, which produced a clean image without noise. When we reformatted the images, it produces 0.5x0.5x1 resolution with 512x512x172 dimension.

Is this sequence good for hippocampal volume estimation and subfield segmentation (also for whole-brain VBM analysis)? Could you please suggest to me a correct sequence, if need to be changed?

Regards Ramesh

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Dear Eugenio and Philipp,

Thank you very much for your suggestions. Could you please give more input on "acquire the T1WI double and average it after coregistration, this increases the SNR".

Should aquire twise the same sequence with 1x1x2 voxel dimension?

Thanks Ramesh

On Fri, 2 Apr, 2021, 9:00 PM Iglesias Gonzalez, Juan E., < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

That all sounds right, thanks a lot Philipp!

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://secure-web.cisco.com/1yAlNRge1To1jCEouu9JnBYJFnIJRo-86GCJ4EIWmAyj8pkk...

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Saemann, Philipp" saemann@psych.mpg.de *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, April 2, 2021 at 03:51 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu, Umesh Rurdrapatna umeshrs@gmail.com *Subject: *Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

•    External Email - Use Caution        *
  
  

Hi,

I try to answer but Eugenio may also add comments. Several points that are important:

• 1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm can

manage.

• Post-aquisition reslicing to a higher resolution does not really

increase the information content. Internally the algorithm works at a much higher resolution, anyway.

• If possible, switch to 3 Tesla.

• If possible and this is a prospective study, add a coronal T2 image and

use the bi-channel option. See papers of Iglesias et al. on this.

• What you could also do on a 1.5 T is acquire the T1WI double and average

it after coregistration, this increases the SNR.

• Generally, isometric resolutions are good due to the symmetry, of course.

• Also on 1.5 T, you may go bit below 1 mm with good head immobilization,

and a longer scanning time. BRAVO in general is a good T1 option.

Best,

Philipp

---

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Ramesh Babu < mgrameshbabu2013@gmail.com> *Gesendet:* Freitag, 2. April 2021 09:29 *An:* Freesurfer support list; Umesh Rurdrapatna *Betreff:* Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

•    External Email - Use Caution        *
  
  

Dear experts,

Sorry for reposting. I am expecting some response from experts, so that I can proceed with confidence.

For our project work, we are looking for hippocampal and its subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with 1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced images with a lot of noise. Then we tried the same sequence with 1x1x2 resolution, and 256x256x80 FOV, which produced a clean image without noise. When we reformatted the images, it produces 0.5x0.5x1 resolution with 512x512x172 dimension.

Is this sequence good for hippocampal volume estimation and subfield segmentation (also for whole-brain VBM analysis)?

Could you please suggest to me a correct sequence, if need to be changed?

Regards

Ramesh _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1IXus-BXNwSxxsWt0Hl4GNJkM1JdHvv3SmnEoV0r7QyM62L...

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Dear Douglas

Thank you very much for your suggestions.

Regards Ramesh

On Tue, 6 Apr, 2021, 7:03 PM Douglas N. Greve, dgreve@mgh.harvard.edu wrote:

Twice the same image at 1x1x1, then use mri_robust_template to register and average them together

On 4/6/2021 8:10 AM, Ramesh Babu wrote:

    External Email - Use Caution

Dear Eugenio and Philipp,

Thank you very much for your suggestions. Could you please give more input on "acquire the T1WI double and average it after coregistration, this increases the SNR".

Should aquire twise the same sequence with 1x1x2 voxel dimension?

Thanks Ramesh

On Fri, 2 Apr, 2021, 9:00 PM Iglesias Gonzalez, Juan E., < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

...

That all sounds right, thanks a lot Philipp!

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1oAFYauOAeFEI_KJ-fkusgflgO_3xjRHgp7o7CJ3qp41OmNY... http://secure-web.cisco.com/1yAlNRge1To1jCEouu9JnBYJFnIJRo-86GCJ4EIWmAyj8pkkdBifGwyirgDc1KI-N6H7_dg4rBnLgE3CaKBeQuxL7GotNy9SzxKSD4OusIQrdGgcD_E0ObeWLPWYbYhFPgBDLEjcGPr-D8PT-k8bLD71quTve1q2fA_-MJY73fb-zPWX2QNDMT39_ceuRLWK8XGl18IGjSIXm6QeDK2erHCdQTO-rww0uRlSIph9mtjeVoEggFnM0sluSy0XceT-MPg9TJwCFg8RuNNq4J20pSw/http%3A%2F%2Fwww.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Saemann, Philipp" saemann@psych.mpg.de *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, April 2, 2021 at 03:51 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu, Umesh Rurdrapatna umeshrs@gmail.com *Subject: *Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

•    External Email - Use Caution        *
  
  

Hi,

I try to answer but Eugenio may also add comments. Several points that are important:

• 1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm can

manage.

• Post-aquisition reslicing to a higher resolution does not really

increase the information content. Internally the algorithm works at a much higher resolution, anyway.

• If possible, switch to 3 Tesla.

• If possible and this is a prospective study, add a coronal T2 image and

use the bi-channel option. See papers of Iglesias et al. on this.

• What you could also do on a 1.5 T is acquire the T1WI double and

average it after coregistration, this increases the SNR.

• Generally, isometric resolutions are good due to the symmetry, of

course.

• Also on 1.5 T, you may go bit below 1 mm with good head immobilization,

and a longer scanning time. BRAVO in general is a good T1 option.

Best,

Philipp

---

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Ramesh Babu < mgrameshbabu2013@gmail.com> *Gesendet:* Freitag, 2. April 2021 09:29 *An:* Freesurfer support list; Umesh Rurdrapatna *Betreff:* Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

•    External Email - Use Caution        *
  
  

Dear experts,

Sorry for reposting. I am expecting some response from experts, so that I can proceed with confidence.

For our project work, we are looking for hippocampal and its subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with 1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced images with a lot of noise. Then we tried the same sequence with 1x1x2 resolution, and 256x256x80 FOV, which produced a clean image without noise. When we reformatted the images, it produces 0.5x0.5x1 resolution with 512x512x172 dimension.

Is this sequence good for hippocampal volume estimation and subfield segmentation (also for whole-brain VBM analysis)?

Could you please suggest to me a correct sequence, if need to be changed?

Regards

Ramesh _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/17suehtrGEpDtQ5EXLhVOfQrRIUslZ-oteK8Gfy-y1RsK9R... https://secure-web.cisco.com/1IXus-BXNwSxxsWt0Hl4GNJkM1JdHvv3SmnEoV0r7QyM62LQaQ7GOor7RtRN0aQzfhFM7lc_9Uu5fcLfv9rDBmaLelquFxD0i5EeJz7dRB1fSkcrH9OXh7CcxyQUdtB4YnGDLHG1bIPRqDN88-MQD4DLOCFxhRwE-yMzpgybXDc7HTRizMdSWlMKBuA-Ut2s6ZjmZ1o1v6hOcCdFt73IOXO-n12alCMDKQF2h4U1gnWzOiaxIt45LuwnOsHIljxgM20xQqjqxBim8X_oH_yng5Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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