External Email - Use Caution
hi, I am trying to reconstruct elephant brain MRI. I am wondering if FreeSurfer can manage this, or does the recon-all command has an inherent bias for human data. Does anyone have an experience using FreeSurfer with a non-human mammal for such purposes?
I have some hopes with this idea, because I am not trying to achieve parcellation or segmentation. Rather, we want to separate White matter from grey Matter, and then probe into various surface measurements across cortical regions. So as per my understanding, all I am expecting from FreeSurfer, is WM-GM segregation, and later (if possible) cortical surface flattening, and DTI.
All words of advice are welcome. Thanks :)
Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391
Hi Malav,
Freesurfer is guided by an atlas that was built from human adult brain images. In the past though, we did have collaborators who have tried some modified versons of the pipeline to work on non-human data. Here are some pointers:
https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData https://hal.archives-ouvertes.fr/hal-01854607/document
As far as I know elephant brain images have not yet been processed. Good luck, Lilla
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Malav Shah malav.shah@bccn-berlin.de Sent: Wednesday, April 6, 2022 1:10 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recontruction of an elephant brain
External Email - Use Caution
hi, I am trying to reconstruct elephant brain MRI. I am wondering if FreeSurfer can manage this, or does the recon-all command has an inherent bias for human data. Does anyone have an experience using FreeSurfer with a non-human mammal for such purposes?
I have some hopes with this idea, because I am not trying to achieve parcellation or segmentation. Rather, we want to separate White matter from grey Matter, and then probe into various surface measurements across cortical regions. So as per my understanding, all I am expecting from FreeSurfer, is WM-GM segregation, and later (if possible) cortical surface flattening, and DTI.
All words of advice are welcome. Thanks :)
Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391
External Email - Use Caution
Hi Lilla,
Thank you so much for your feedback.
I completely understand the tool's bias for human brains. As you said, the elephant brain images are not well understood so far. We aim to take initial steps in that direction, starting with small goals like WM-GM seperation, cortical thickness measurements, and surface visualisation with flattening. Do you think it can be achieved with FreeSurfer's volume-based analysis pipeline? We would be more than happy to collaborate on that.
Looking forward to hearing from you :) Thanks and regards, Malav Shah
From: "Zollei, Lilla,Ph.D." LZOLLEI@MGH.HARVARD.EDU To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 6, 2022 8:29:33 PM Subject: Re: [Freesurfer] recontruction of an elephant brain
Hi Malav,
Freesurfer is guided by an atlas that was built from human adult brain images. In the past though, we did have collaborators who have tried some modified versons of the pipeline to work on non-human data. Here are some pointers:
[ https://secure-web.cisco.com/1149bxkRGOm5AzvVYmA-Bxc160t7HU-wHF-xUFdBZaQ-CBD... | https://secure-web.cisco.com/1149bxkRGOm5AzvVYmA-Bxc160t7HU-wHF-xUFdBZaQ-CBD... ] [ https://secure-web.cisco.com/1hWAtvKnqtTh7X5HFZdRhQKvG5qfkbftxeOlgW8K8ZQVAWK... | https://secure-web.cisco.com/1hWAtvKnqtTh7X5HFZdRhQKvG5qfkbftxeOlgW8K8ZQVAWK... ]
As far as I know elephant brain images have not yet been processed. G ood luck, Lilla
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Malav Shah malav.shah@bccn-berlin.de Sent: Wednesday, April 6, 2022 1:10 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recontruction of an elephant brain
External Email - Use Caution
hi, I am trying to reconstruct elephant brain MRI. I am wondering if FreeSurfer can manage this, or does the recon-all command has an inherent bias for human data. Does anyone have an experience using FreeSurfer with a non-human mammal for such purposes?
I have some hopes with this idea, because I am not trying to achieve parcellation or segmentation. Rather, we want to separate White matter from grey Matter, and then probe into various surface measurements across cortical regions. So as per my understanding, all I am expecting from FreeSurfer, is WM-GM segregation, and later (if possible) cortical surface flattening, and DTI.
All words of advice are welcome. Thanks :)
Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1RoEboCpHmvPs2HeTL8Nb0v8v9xIua0Av8gEaEpSCnIBilZ... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1ia2YaE62d9i3ksVrQFJ8Hek5pDsEs6SQVFRH00n-FNXdiL... https://secure-web.cisco.com/1ia2YaE62d9i3ksVrQFJ8Hek5pDsEs6SQVFRH00n-FNXdiL3dmXsOOsUFN2NvkiyEdR5oBgpSYaR9t8aa1ISQPiNv0685pWZ3YTZGbVgP5IKFIWS_mRonP_JaEmHK7nEdbQwjjZpIGqoqOcNlSWoSYMY4ObKmOyEi-bgI7WaUveNIho2-2hsCSF9TPyXBUeevuMyflzGzDl3Az1BI8YeD_fco6qNg8iHxDnydgUAs1v8PzCrMMdf6pbKT8cRn5SX94OJAtym1e14oRGr5reYGNLSJnEoBk0kGwSdp7yKdiaaHgFXZmUvjgXdpqhymI8c_OzlwVNlkt8ju4eEA-mjJbg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Lot's of people have adapted FS to non-human brains, just google it. For surface analysis, you need to get the "subcortical mass" -- the equivalent to the filled.mgz. This is the cerebral white matter + subcort gray structures. Once you have that, you might be able to run mris_place_surfaces. I'd have to walk you through the options to use or not.
On 4/8/2022 6:01 AM, Malav Shah wrote:
External Email - Use Caution
Hi Lilla,
Thank you so much for your feedback.
I completely understand the tool's bias for human brains. As you said, the elephant brain images are not well understood so far. We aim to take initial steps in that direction, starting with small goals like WM-GM seperation, cortical thickness measurements, and surface visualisation with flattening. Do you think it can be achieved with FreeSurfer's volume-based analysis pipeline? We would be more than happy to collaborate on that.
Looking forward to hearing from you :) Thanks and regards, Malav Shah
*From: *"Zollei, Lilla,Ph.D." LZOLLEI@MGH.HARVARD.EDU *To: *"freesurfer" freesurfer@nmr.mgh.harvard.edu *Sent: *Wednesday, April 6, 2022 8:29:33 PM *Subject: *Re: [Freesurfer] recontruction of an elephant brain
Hi Malav,
Freesurfer is guided by an atlas that was built from human adult brain images. In the past though, we did have collaborators who have tried some modified versons of the pipeline to work on non-human data. Here are some pointers:
*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData https://secure-web.cisco.com/1149bxkRGOm5AzvVYmA-Bxc160t7HU-wHF-xUFdBZaQ-CBDMhfyoMiEkF7LgJIJ_w2ZHvZc48UMSj3dntsS0oSNQ8vdQc73Jlmd34JnP5adcUaLvPSYD34MknD4RGJCciLXDv6LLLWHftORNu5-I2UJ9s-3vmM0xvwEOg_rP6R_H06ZkjIIqqSlghgO6dQWO2TD0avKyXnSU_eDy0zm0jtaUQQo_9wjJxYXzzbruHepTSyu0mPr2m1plsCrh1oqcnOIO52xQ59mJxjJHGSSG0NSkfLM9x7-WkZswQgb9jyx13SmLAfd8qay-lglviBvnwJnizBfEJwrJyEuIJ53mdzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMonkeyData *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://hal.archives-ouvertes.fr/hal-01854607/document https://secure-web.cisco.com/1hWAtvKnqtTh7X5HFZdRhQKvG5qfkbftxeOlgW8K8ZQVAWK819JdXTeTLKb0ZBsyMLy1VhpeygvLjaYwwxrmYVPViJNnTZZi9lFJE3tW0UOfiyDRYL7LSqSBBf_ZQy7aj0eQky-xkHYta4Qae7thrJY6l-1EknyGByegvwFwKtaWKUyOVnMP4pNqYPVIf_dHiu63tvct2_QXvF24hUJ9sZhtopGTpdD9PDpBB3ZLYnfZ2eE2exZkaEVnyBVavesE8Realx7SY17iZbjmtmZ6kmQtoDEkBoGHiN562LEyksb8hPFBCewiJJYH3lwGBNbpE7Z3s9FRtJyE2hkb4z5uzTQ/https%3A%2F%2Fhal.archives-ouvertes.fr%2Fhal-01854607%2Fdocument
As far as I know elephant brain images have not yet been processed. Good luck, Lilla
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Malav Shah malav.shah@bccn-berlin.de *Sent:* Wednesday, April 6, 2022 1:10 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] recontruction of an elephant brain
External Email - Use Caution
hi, I am trying to reconstruct elephant brain MRI. I am wondering if FreeSurfer can manage this, or does the recon-all command has an inherent bias for human data. Does anyone have an experience using FreeSurfer with a non-human mammal for such purposes?
I have some hopes with this idea, because I am not trying to achieve parcellation or segmentation. Rather, we want to separate White matter from grey Matter, and then probe into various surface measurements across cortical regions. So as per my understanding, all I am expecting from FreeSurfer, is WM-GM segregation, and later (if possible) cortical surface flattening, and DTI.
All words of advice are welcome. Thanks :)
Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391
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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline https://www.massgeneralbrigham.org/complianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Douglas, thank you so much for your suggestions. Your understanding of my task is very precise, and I would love to move in the direction you recommend. I would appreciate a bit more detailed guidance. Would you have a little bit of time to spare for me in those regards?
Looking foward, Malav Shah
From: "Douglas N. Greve" dgreve@mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 9, 2022 10:18:18 PM Subject: Re: [Freesurfer] recontruction of an elephant brain
Lot's of people have adapted FS to non-human brains, just google it. For surface analysis, you need to get the "subcortical mass" -- the equivalent to the filled.mgz. This is the cerebral white matter + subcort gray structures. Once you have that, you might be able to run mris_place_surfaces. I'd have to walk you through the options to use or not.
On 4/8/2022 6:01 AM, Malav Shah wrote:
External Email - Use Caution Hi Lilla,
Thank you so much for your feedback.
I completely understand the tool's bias for human brains. As you said, the elephant brain images are not well understood so far. We aim to take initial steps in that direction, starting with small goals like WM-GM seperation, cortical thickness measurements, and surface visualisation with flattening. Do you think it can be achieved with FreeSurfer's volume-based analysis pipeline? We would be more than happy to collaborate on that.
Looking forward to hearing from you :) Thanks and regards, Malav Shah
From: "Zollei, Lilla,Ph.D." [ mailto:LZOLLEI@MGH.HARVARD.EDU | LZOLLEI@MGH.HARVARD.EDU ] To: "freesurfer" [ mailto:freesurfer@nmr.mgh.harvard.edu | freesurfer@nmr.mgh.harvard.edu ] Sent: Wednesday, April 6, 2022 8:29:33 PM Subject: Re: [Freesurfer] recontruction of an elephant brain
Hi Malav,
Freesurfer is guided by an atlas that was built from human adult brain images. In the past though, we did have collaborators who have tried some modified versons of the pipeline to work on non-human data. Here are some pointers:
[ https://secure-web.cisco.com/1149bxkRGOm5AzvVYmA-Bxc160t7HU-wHF-xUFdBZaQ-CBD... | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ExzD0__PM1Mq7A_-8gKPzWKtisVlALcDFOcYwUpt0CMLc8... ] [ https://secure-web.cisco.com/1hWAtvKnqtTh7X5HFZdRhQKvG5qfkbftxeOlgW8K8ZQVAWK... | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZQ1hYFTjRv8_0udFozzAyv7n8WkJc_4tINMw_gJRl6OsnS... ]
As far as I know elephant brain images have not yet been processed. G ood luck, Lilla
From: [ mailto:freesurfer-bounces@nmr.mgh.harvard.edu | freesurfer-bounces@nmr.mgh.harvard.edu ] [ mailto:freesurfer-bounces@nmr.mgh.harvard.edu | freesurfer-bounces@nmr.mgh.harvard.edu ] on behalf of Malav Shah [ mailto:malav.shah@bccn-berlin.de | malav.shah@bccn-berlin.de ] Sent: Wednesday, April 6, 2022 1:10 PM To: [ mailto:freesurfer@nmr.mgh.harvard.edu | freesurfer@nmr.mgh.harvard.edu ] [ mailto:freesurfer@nmr.mgh.harvard.edu | freesurfer@nmr.mgh.harvard.edu ] Subject: [Freesurfer] recontruction of an elephant brain
External Email - Use Caution hi, I am trying to reconstruct elephant brain MRI. I am wondering if FreeSurfer can manage this, or does the recon-all command has an inherent bias for human data. Does anyone have an experience using FreeSurfer with a non-human mammal for such purposes?
I have some hopes with this idea, because I am not trying to achieve parcellation or segmentation. Rather, we want to separate White matter from grey Matter, and then probe into various surface measurements across cortical regions. So as per my understanding, all I am expecting from FreeSurfer, is WM-GM segregation, and later (if possible) cortical surface flattening, and DTI.
All words of advice are welcome. Thanks :)
Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391
_______________________________________________ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] [ https://secure-web.cisco.com/1cRrd7pAcwEiUrL4DaF9c57C_kBjR2fNvG6tWr50XZ5xkNV... | https://secure-web.cisco.com/1cRrd7pAcwEiUrL4DaF9c57C_kBjR2fNvG6tWr50XZ5xkNV... ] 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 Mass General Brigham Compliance HelpLine at [ https://secure-web.cisco.com/1_VSCO8R0plzvpBjkQ8ER6u15b1z-6hnpYbnaasuBy9DDtN... | https://secure-web.cisco.com/1_VSCO8R0plzvpBjkQ8ER6u15b1z-6hnpYbnaasuBy9DDtN... ] [ https://secure-web.cisco.com/1_VSCO8R0plzvpBjkQ8ER6u15b1z-6hnpYbnaasuBy9DDtN... | https://secure-web.cisco.com/1_VSCO8R0plzvpBjkQ8ER6u15b1z-6hnpYbnaasuBy9DDtNkv6_AT3DoZMdS3c7DN2qbpzXRKg53Obld4HyGPd_XzPZM7oTnyDyH6hGytm3z-7IGKG5pDQh8a_-yUwA9Du2AkT0rrW9OTeSV37Dzio2GIaaKsWU5oTc3PnKFNcn0_rs8Hzy1eSlHXmOmN7Lxvu5UbHgHrwMCk6ANBnYzuQ32gfLtyMcn-OBKj8Q_TA9m7_2WnvQc3AFgsKCIUhq3Iyn9efw2APeUAw3n4hSL5GtNPHt62p162Ik_v51-Va4Qnatg4xP6bcxjQ1YkdkbxC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline ] . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
_______________________________________________ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] [ https://secure-web.cisco.com/1cRrd7pAcwEiUrL4DaF9c57C_kBjR2fNvG6tWr50XZ5xkNV... | https://secure-web.cisco.com/1cRrd7pAcwEiUrL4DaF9c57C_kBjR2fNvG6tWr50XZ5xkNV... ]
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1cRrd7pAcwEiUrL4DaF9c57C_kBjR2fNvG6tWr50XZ5xkNV... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1_VSCO8R0plzvpBjkQ8ER6u15b1z-6hnpYbnaasuBy9DDtN... https://secure-web.cisco.com/1_VSCO8R0plzvpBjkQ8ER6u15b1z-6hnpYbnaasuBy9DDtNkv6_AT3DoZMdS3c7DN2qbpzXRKg53Obld4HyGPd_XzPZM7oTnyDyH6hGytm3z-7IGKG5pDQh8a_-yUwA9Du2AkT0rrW9OTeSV37Dzio2GIaaKsWU5oTc3PnKFNcn0_rs8Hzy1eSlHXmOmN7Lxvu5UbHgHrwMCk6ANBnYzuQ32gfLtyMcn-OBKj8Q_TA9m7_2WnvQc3AFgsKCIUhq3Iyn9efw2APeUAw3n4hSL5GtNPHt62p162Ik_v51-Va4Qnatg4xP6bcxjQ1YkdkbxC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
External Email - Use Caution
Hi Dr. Greve, I send a gentle reminder, in case the previous mail skipped your attention. with regards, Malav
From: "Malav Shah" malav.shah@bccn-berlin.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 12, 2022 3:08:50 PM Subject: Re: [Freesurfer] recontruction of an elephant brain
Hi Douglas, thank you so much for your suggestions. Your understanding of my task is very precise, and I would love to move in the direction you recommend. I would appreciate a bit more detailed guidance. Would you have a little bit of time to spare for me in those regards?
Looking foward, Malav Shah
From: "Douglas N. Greve" dgreve@mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 9, 2022 10:18:18 PM Subject: Re: [Freesurfer] recontruction of an elephant brain
Lot's of people have adapted FS to non-human brains, just google it. For surface analysis, you need to get the "subcortical mass" -- the equivalent to the filled.mgz. This is the cerebral white matter + subcort gray structures. Once you have that, you might be able to run mris_place_surfaces. I'd have to walk you through the options to use or not.
On 4/8/2022 6:01 AM, Malav Shah wrote:
External Email - Use Caution Hi Lilla,
Thank you so much for your feedback.
I completely understand the tool's bias for human brains. As you said, the elephant brain images are not well understood so far. We aim to take initial steps in that direction, starting with small goals like WM-GM seperation, cortical thickness measurements, and surface visualisation with flattening. Do you think it can be achieved with FreeSurfer's volume-based analysis pipeline? We would be more than happy to collaborate on that.
Looking forward to hearing from you :) Thanks and regards, Malav Shah
From: "Zollei, Lilla,Ph.D." [ mailto:LZOLLEI@MGH.HARVARD.EDU | LZOLLEI@MGH.HARVARD.EDU ] To: "freesurfer" [ mailto:freesurfer@nmr.mgh.harvard.edu | freesurfer@nmr.mgh.harvard.edu ] Sent: Wednesday, April 6, 2022 8:29:33 PM Subject: Re: [Freesurfer] recontruction of an elephant brain
Hi Malav,
Freesurfer is guided by an atlas that was built from human adult brain images. In the past though, we did have collaborators who have tried some modified versons of the pipeline to work on non-human data. Here are some pointers:
[ https://secure-web.cisco.com/1149bxkRGOm5AzvVYmA-Bxc160t7HU-wHF-xUFdBZaQ-CBD... | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/15zKcPfHpUcGY710CqXKgtYibKZyu0LEt5GXwxUAAgoYrbO... ] [ https://secure-web.cisco.com/1hWAtvKnqtTh7X5HFZdRhQKvG5qfkbftxeOlgW8K8ZQVAWK... | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10rrx4lWP8J7VXgoRrw4EitUlYSbiRC_Io0YoSF_V3J91y9... ]
As far as I know elephant brain images have not yet been processed. G ood luck, Lilla
From: [ mailto:freesurfer-bounces@nmr.mgh.harvard.edu | freesurfer-bounces@nmr.mgh.harvard.edu ] [ mailto:freesurfer-bounces@nmr.mgh.harvard.edu | freesurfer-bounces@nmr.mgh.harvard.edu ] on behalf of Malav Shah [ mailto:malav.shah@bccn-berlin.de | malav.shah@bccn-berlin.de ] Sent: Wednesday, April 6, 2022 1:10 PM To: [ mailto:freesurfer@nmr.mgh.harvard.edu | freesurfer@nmr.mgh.harvard.edu ] [ mailto:freesurfer@nmr.mgh.harvard.edu | freesurfer@nmr.mgh.harvard.edu ] Subject: [Freesurfer] recontruction of an elephant brain
External Email - Use Caution hi, I am trying to reconstruct elephant brain MRI. I am wondering if FreeSurfer can manage this, or does the recon-all command has an inherent bias for human data. Does anyone have an experience using FreeSurfer with a non-human mammal for such purposes?
I have some hopes with this idea, because I am not trying to achieve parcellation or segmentation. Rather, we want to separate White matter from grey Matter, and then probe into various surface measurements across cortical regions. So as per my understanding, all I am expecting from FreeSurfer, is WM-GM segregation, and later (if possible) cortical surface flattening, and DTI.
All words of advice are welcome. Thanks :)
Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391
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HI Malav, did you create the subcortical mass? Have you separated the hemispheres?
On 4/18/2022 4:48 PM, Malav Shah wrote:
External Email - Use Caution
Hi Dr. Greve, I send a gentle reminder, in case the previous mail skipped your attention. with regards, Malav
*From: *"Malav Shah" malav.shah@bccn-berlin.de *To: *"Freesurfer support list" freesurfer@nmr.mgh.harvard.edu *Sent: *Tuesday, April 12, 2022 3:08:50 PM *Subject: *Re: [Freesurfer] recontruction of an elephant brain
Hi Douglas, thank you so much for your suggestions. Your understanding of my task is very precise, and I would love to move in the direction you recommend. I would appreciate a bit more detailed guidance. Would you have a little bit of time to spare for me in those regards?
Looking foward, Malav Shah
*From: *"Douglas N. Greve" dgreve@mgh.harvard.edu *To: *"freesurfer" freesurfer@nmr.mgh.harvard.edu *Sent: *Saturday, April 9, 2022 10:18:18 PM *Subject: *Re: [Freesurfer] recontruction of an elephant brain
Lot's of people have adapted FS to non-human brains, just google it. For surface analysis, you need to get the "subcortical mass" -- the equivalent to the filled.mgz. This is the cerebral white matter + subcort gray structures. Once you have that, you might be able to run mris_place_surfaces. I'd have to walk you through the options to use or not.
On 4/8/2022 6:01 AM, Malav Shah wrote:
External Email - Use Caution Hi Lilla, Thank you so much for your feedback. I completely understand the tool's bias for human brains. As you said, the elephant brain images are not well understood so far. We aim to take initial steps in that direction, starting with small goals like WM-GM seperation, cortical thickness measurements, and surface visualisation with flattening. Do you think it can be achieved with FreeSurfer's volume-based analysis pipeline? We would be more than happy to collaborate on that. Looking forward to hearing from you :) Thanks and regards, Malav Shah ------------------------------------------------------------------------ *From: *"Zollei, Lilla,Ph.D." <LZOLLEI@MGH.HARVARD.EDU> <mailto:LZOLLEI@MGH.HARVARD.EDU> *To: *"freesurfer" <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Sent: *Wednesday, April 6, 2022 8:29:33 PM *Subject: *Re: [Freesurfer] recontruction of an elephant brain Hi Malav, Freesurfer is guided by an atlas that was built from human adult brain images. In the past though, we did have collaborators who have tried some modified versons of the pipeline to work on non-human data. Here are some pointers: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData <https://secure-web.cisco.com/1149bxkRGOm5AzvVYmA-Bxc160t7HU-wHF-xUFdBZaQ-CBDMhfyoMiEkF7LgJIJ_w2ZHvZc48UMSj3dntsS0oSNQ8vdQc73Jlmd34JnP5adcUaLvPSYD34MknD4RGJCciLXDv6LLLWHftORNu5-I2UJ9s-3vmM0xvwEOg_rP6R_H06ZkjIIqqSlghgO6dQWO2TD0avKyXnSU_eDy0zm0jtaUQQo_9wjJxYXzzbruHepTSyu0mPr2m1plsCrh1oqcnOIO52xQ59mJxjJHGSSG0NSkfLM9x7-WkZswQgb9jyx13SmLAfd8qay-lglviBvnwJnizBfEJwrJyEuIJ53mdzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMonkeyData> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://hal.archives-ouvertes.fr/hal-01854607/document <https://secure-web.cisco.com/1hWAtvKnqtTh7X5HFZdRhQKvG5qfkbftxeOlgW8K8ZQVAWK819JdXTeTLKb0ZBsyMLy1VhpeygvLjaYwwxrmYVPViJNnTZZi9lFJE3tW0UOfiyDRYL7LSqSBBf_ZQy7aj0eQky-xkHYta4Qae7thrJY6l-1EknyGByegvwFwKtaWKUyOVnMP4pNqYPVIf_dHiu63tvct2_QXvF24hUJ9sZhtopGTpdD9PDpBB3ZLYnfZ2eE2exZkaEVnyBVavesE8Realx7SY17iZbjmtmZ6kmQtoDEkBoGHiN562LEyksb8hPFBCewiJJYH3lwGBNbpE7Z3s9FRtJyE2hkb4z5uzTQ/https%3A%2F%2Fhal.archives-ouvertes.fr%2Fhal-01854607%2Fdocument> As far as I know elephant brain images have not yet been processed. Good luck, Lilla ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Malav Shah <malav.shah@bccn-berlin.de> <mailto:malav.shah@bccn-berlin.de> *Sent:* Wednesday, April 6, 2022 1:10 PM *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* [Freesurfer] recontruction of an elephant brain External Email - Use Caution hi, I am trying to reconstruct elephant brain MRI. I am wondering if FreeSurfer can manage this, or does the recon-all command has an inherent bias for human data. Does anyone have an experience using FreeSurfer with a non-human mammal for such purposes? I have some hopes with this idea, because I am not trying to achieve parcellation or segmentation. Rather, we want to separate White matter from grey Matter, and then probe into various surface measurements across cortical regions. So as per my understanding, all I am expecting from FreeSurfer, is WM-GM segregation, and later (if possible) cortical surface flattening, and DTI. All words of advice are welcome. Thanks :) Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. 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Douglas N. Greve -
Malav Shah -
Zollei, Lilla,Ph.D.