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Hello,
I am working on project using Freesurfer’s “Segmentation of hippocampal subfields and nuclei of the amygdala” to segment the hippocampal subfields and compare it with a software called ASHS developed by the Penn Image Computing and Science Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w SPC vNav.08 iso, ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to run the command: segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal sequence so to compare the two outputs, it would be ideal to also use the HighRes Hippocampal sequence.
Please let me know if you need additional information.
Thanks,
Joshua E. Pasaye, B.S. (he/him/his) Clinical Research Coordinator | Imaging Core Mesulam Center for Cognitive Neurology and Alzheimer's Disease Northwestern University – Feinberg School of Medicine 300 E. Superior Street, Tarry 8-734, Chicago, IL 60611 (312) 503-5675 | joshua.pasaye@northwestern.edumailto:joshua.pasaye@northwestern.edu
Dear Joshua, This is a bit of an empirical question. I’d totally run both on a few subjects and compare the results. If you do so: I would selfishly/greatly appreciate it if you shared your impressions with me :-) Cheers, /Eugenio
-- Juan Eugenio Iglesias http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Joshua Ezequiel Pasaye joshua.pasaye@northwestern.edu Date: Friday, November 17, 2023 at 11:46 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala
External Email - Use Caution Hello,
I am working on project using Freesurfer’s “Segmentation of hippocampal subfields and nuclei of the amygdala” to segment the hippocampal subfields and compare it with a software called ASHS developed by the Penn Image Computing and Science Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w SPC vNav.08 iso, ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to run the command: segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal sequence so to compare the two outputs, it would be ideal to also use the HighRes Hippocampal sequence.
Please let me know if you need additional information.
Thanks,
Joshua E. Pasaye, B.S. (he/him/his) Clinical Research Coordinator | Imaging Core Mesulam Center for Cognitive Neurology and Alzheimer's Disease Northwestern University – Feinberg School of Medicine 300 E. Superior Street, Tarry 8-734, Chicago, IL 60611 (312) 503-5675 | joshua.pasaye@northwestern.edumailto:joshua.pasaye@northwestern.edu
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Dear Dr. Iglesias,
Thank you for your quick response and insight. I wanted to make sure that there were not any specific requirements for the T2w scan when using the segmentation command. I will try both and let you know my thoughts.
Kindly,
Joshua E. Pasaye, B.S. (he/him/his) Clinical Research Coordinator | Imaging Core Mesulam Center for Cognitive Neurology and Alzheimer's Disease Northwestern University – Feinberg School of Medicine 300 E. Superior Street, Tarry 8-734, Chicago, IL 60611 (312) 503-5675 | joshua.pasaye@northwestern.edumailto:joshua.pasaye@northwestern.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Date: Friday, November 17, 2023 at 2:48 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala Dear Joshua, This is a bit of an empirical question. I’d totally run both on a few subjects and compare the results. If you do so: I would selfishly/greatly appreciate it if you shared your impressions with me :-) Cheers, /Eugenio
-- Juan Eugenio Iglesias http://secure-web.cisco.com/1AgZJS_lt0DLao4RNJQjdUp6--s94lZQRuhY7Nebh6-r-Klm...https://secure-web.cisco.com/18e9gJX6afySE6laab4_aEvzM3e1UdoOMJaafEuz5sVRyGTlFkx5HMzj3RrSws9n3Rr_c87LNwY1koW_zkas-d2TvbDCzjPBIIsAnCpFZ0hmXSyGb8byTU1Y_SRVzJvWyA97Kv4o6_umAYWYy6WhDUyqCoqJUiobHty-1oR_4anl7GjWYTdIbl84hQPsaCosYBqW8J-8yba1uIKxu0tzE0dFrze8SvuznbXaAASpNteEF7o_l-V62-yae8EzAWJ6_Zwb7h_1ZDUPZdXCYwV1rM-4oChWEeTBzdmedijTlNYP3F-xbUifgmZsdivJJoSOY/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fwww.jeiglesias.com__;!!Dq0X2DkFhyF93HkjWTBQKhk!XGRVYnfjnbsjimlASVuNyHlIzkIPPRysPMLOlCR5cFgkMD0R_BgtOSseL2_gqxFHJ_dKyXuOIYfEg2f0kzPAtGtfQfHxHYA3bPzmwdLrPobcOA$
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Joshua Ezequiel Pasaye joshua.pasaye@northwestern.edu Date: Friday, November 17, 2023 at 11:46 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala
External Email - Use Caution Hello,
I am working on project using Freesurfer’s “Segmentation of hippocampal subfields and nuclei of the amygdala” to segment the hippocampal subfields and compare it with a software called ASHS developed by the Penn Image Computing and Science Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w SPC vNav.08 iso, ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to run the command: segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal sequence so to compare the two outputs, it would be ideal to also use the HighRes Hippocampal sequence.
Please let me know if you need additional information.
Thanks,
Joshua E. Pasaye, B.S. (he/him/his) Clinical Research Coordinator | Imaging Core Mesulam Center for Cognitive Neurology and Alzheimer's Disease Northwestern University – Feinberg School of Medicine 300 E. Superior Street, Tarry 8-734, Chicago, IL 60611 (312) 503-5675 | joshua.pasaye@northwestern.edumailto:joshua.pasaye@northwestern.edu
freesurfer@nmr.mgh.harvard.edu
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Iglesias Gonzalez, Juan E. -
Joshua Ezequiel Pasaye