External Email - Use Caution
Dear Freesurfer developers, In the link below, you see two brains belonging to the same subject:
https://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ftv... [https://secure-web.cisco.com/1B08cXHTWamf2XLl-Do2M2Y2jFkmx7hn93F8dK1GfF1Mv6r...https://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ftvuT3XYGAkTFceTbXiWCr6SNywbE8fcYjdVjN5ilNvHSmxSGWIlJ4e3EY93BEtyFovUNqHiubNxANK-VQkFfB08mlvWdjOSDrAj3wpUGTOU4bDhdASUiFNGP3Qr6iVkC6Mr5aZDXf0TB1KFC1LIM6XdLNKt6h9H-u-IBO9Tk52el1Mw-uU6vhDGCP9KJm0YdqioUjFCwFe1WFkE0tIdCRPJnnO0uVbXkZZq-gGKQJ8ipLvzHCK3PRTeWj5ov49VwfX4K8fJXSq-InNeWjDBXeaxgchX-rw7zfFyreXocJw/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0 Screen Shot 2022-01-26 at 1.40.23 PM.pnghttps://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ftvuT3XYGAkTFceTbXiWCr6SNywbE8fcYjdVjN5ilNvHSmxSGWIlJ4e3EY93BEtyFovUNqHiubNxANK-VQkFfB08mlvWdjOSDrAj3wpUGTOU4bDhdASUiFNGP3Qr6iVkC6Mr5aZDXf0TB1KFC1LIM6XdLNKt6h9H-u-IBO9Tk52el1Mw-uU6vhDGCP9KJm0YdqioUjFCwFe1WFkE0tIdCRPJnnO0uVbXkZZq-gGKQJ8ipLvzHCK3PRTeWj5ov49VwfX4K8fJXSq-InNeWjDBXeaxgchX-rw7zfFyreXocJw/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0 Shared with Dropbox http://secure-web.cisco.com/1qgxtofGxpoR7Sqc5YpeFwa6ndZVhgCVEL8DwdalIfXi80qU...
while one of them is reconstructed with FS7.2, the other one is reconstructed with a pipeline that uses another code for extracting brain tissue (BET Mask) and then use FS6 for the remaining stages of the reconstruction.
While the final result of both constructions matches in most aspects, they don't occupy the same coordinates in space. Is there a way that we can match the coordinates of each voxel for two images? Or in other words make them compatible.
The Platform we use is CentOS7 .
Thanks and all the best, Ela
External Email - Use Caution
Hi all,
I just wanted to follow-up on this message with one extra piece of information added:
The two brains are exactly identical. Considering that we have two identical reconstructed brains (exactly the same as each other), with the only difference being that one of them is a little bit shifted and rotated in comparison to the other one, if there a way to measure the amount of this rotation and shift? If yes, can this information be used to counteract this rotation and shift? In other words, can we rotate and shift the second brain back in the exact opposite direction, so it completely overlays the first brain using freesurfer?
Thank you and all the best, Ela ________________________________ From: Salar Dini, Elaheh Sent: Monday, January 31, 2022 6:46 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Recon-all reconstructed image coordinates
Dear Freesurfer developers, In the link below, you see two brains belonging to the same subject:
https://secure-web.cisco.com/1NWflVFwpPzLHCFaPUaWGJm7LXUzRcOtfnS1v2S2jf9YnLt... [https://secure-web.cisco.com/1j-G-TuRKXU4iWWHZ4wv13XW3o-r7U206GNIBYvUF56HJFU...https://secure-web.cisco.com/1NWflVFwpPzLHCFaPUaWGJm7LXUzRcOtfnS1v2S2jf9YnLt6Rzus9ZuAZ6xJTpf6y9xO9P3iTGNemM60KZruigxVGVmaFQs62kgRbwS1E6Mo1eZwTzNZowsX0acdSHsL56-BRum1pT8OQRTExS-IW86GzaedHOgl4a-FSBcijH6_xAJUq83RNXgPDCKsuQtJh8Un1OIZG6GNCOs8JgwPNSftmFoSk0saftI2OMSsgZaNtkF8LxY25PCtxLQJ5nuQJdAM6vpkq9U4KMuH9de5NMoicfg2OgOh6UnOH8-KwcZSBUxt6CBz4_GMdKk0a2yZUy1N7ATye9d6rPF3k6VsCFw/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0 Screen Shot 2022-01-26 at 1.40.23 PM.pnghttps://secure-web.cisco.com/1NWflVFwpPzLHCFaPUaWGJm7LXUzRcOtfnS1v2S2jf9YnLt6Rzus9ZuAZ6xJTpf6y9xO9P3iTGNemM60KZruigxVGVmaFQs62kgRbwS1E6Mo1eZwTzNZowsX0acdSHsL56-BRum1pT8OQRTExS-IW86GzaedHOgl4a-FSBcijH6_xAJUq83RNXgPDCKsuQtJh8Un1OIZG6GNCOs8JgwPNSftmFoSk0saftI2OMSsgZaNtkF8LxY25PCtxLQJ5nuQJdAM6vpkq9U4KMuH9de5NMoicfg2OgOh6UnOH8-KwcZSBUxt6CBz4_GMdKk0a2yZUy1N7ATye9d6rPF3k6VsCFw/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0 Shared with Dropbox http://secure-web.cisco.com/1zkZ6eB_aOa5fOlAVIrf-e3jHDmQL2iWHEKUnKlJMz6lXJkN...
while one of them is reconstructed with FS7.2, the other one is reconstructed with a pipeline that uses another code for extracting brain tissue (BET Mask) and then use FS6 for the remaining stages of the reconstruction.
While the final result of both constructions matches in most aspects, they don't occupy the same coordinates in space. Is there a way that we can match the coordinates of each voxel for two images? Or in other words make them compatible.
The Platform we use is CentOS7 .
Thanks and all the best, Ela
You can try registering them together like mri_coreg ---mov betmaskvolume.nii.gz --targ orig.mgz --reg reg.lta Then mri_vol2vol --mov betmaskvol.nii.gz --targ orig.mgz --reg.lta --o betmask-in-fs.mgz --interp nearest The betmaskvol should be the intensity image (like orig.mgz) and not a binary mask or segmentation
On 2/2/2022 4:05 PM, Salar Dini, Elaheh wrote:
External Email - Use Caution
Hi all,
I just wanted to follow-up on this message with one extra piece of information added:
The two brains are exactly identical. Considering that we have two identical reconstructed brains (exactly the same as each other), with the only difference being that one of them is a little bit shifted and rotated in comparison to the other one, if there a way to measure the amount of this rotation and shift? If yes, can this information be used to counteract this rotation and shift? In other words, can we rotate and shift the second brain back in the exact opposite direction, so it completely overlays the first brain using freesurfer?
Thank you and all the best, Ela
*From:* Salar Dini, Elaheh *Sent:* Monday, January 31, 2022 6:46 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Recon-all reconstructed image coordinates Dear Freesurfer developers, In the link below, you see two brains belonging to the same subject:
*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.dropbox.com/s/c2gsp8h8jj7c93d/Screen%20Shot%202022-01-26%20at%20... https://secure-web.cisco.com/1NWflVFwpPzLHCFaPUaWGJm7LXUzRcOtfnS1v2S2jf9YnLt6Rzus9ZuAZ6xJTpf6y9xO9P3iTGNemM60KZruigxVGVmaFQs62kgRbwS1E6Mo1eZwTzNZowsX0acdSHsL56-BRum1pT8OQRTExS-IW86GzaedHOgl4a-FSBcijH6_xAJUq83RNXgPDCKsuQtJh8Un1OIZG6GNCOs8JgwPNSftmFoSk0saftI2OMSsgZaNtkF8LxY25PCtxLQJ5nuQJdAM6vpkq9U4KMuH9de5NMoicfg2OgOh6UnOH8-KwcZSBUxt6CBz4_GMdKk0a2yZUy1N7ATye9d6rPF3k6VsCFw/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0 https://secure-web.cisco.com/1NWflVFwpPzLHCFaPUaWGJm7LXUzRcOtfnS1v2S2jf9YnLt6Rzus9ZuAZ6xJTpf6y9xO9P3iTGNemM60KZruigxVGVmaFQs62kgRbwS1E6Mo1eZwTzNZowsX0acdSHsL56-BRum1pT8OQRTExS-IW86GzaedHOgl4a-FSBcijH6_xAJUq83RNXgPDCKsuQtJh8Un1OIZG6GNCOs8JgwPNSftmFoSk0saftI2OMSsgZaNtkF8LxY25PCtxLQJ5nuQJdAM6vpkq9U4KMuH9de5NMoicfg2OgOh6UnOH8-KwcZSBUxt6CBz4_GMdKk0a2yZUy1N7ATye9d6rPF3k6VsCFw/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0
Screen Shot 2022-01-26 at 1.40.23 PM.png https://secure-web.cisco.com/1NWflVFwpPzLHCFaPUaWGJm7LXUzRcOtfnS1v2S2jf9YnLt6Rzus9ZuAZ6xJTpf6y9xO9P3iTGNemM60KZruigxVGVmaFQs62kgRbwS1E6Mo1eZwTzNZowsX0acdSHsL56-BRum1pT8OQRTExS-IW86GzaedHOgl4a-FSBcijH6_xAJUq83RNXgPDCKsuQtJh8Un1OIZG6GNCOs8JgwPNSftmFoSk0saftI2OMSsgZaNtkF8LxY25PCtxLQJ5nuQJdAM6vpkq9U4KMuH9de5NMoicfg2OgOh6UnOH8-KwcZSBUxt6CBz4_GMdKk0a2yZUy1N7ATye9d6rPF3k6VsCFw/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0 Shared with Dropbox www.dropbox.com
while one of them is reconstructed with FS7.2, the other one is reconstructed with a pipeline that uses another code for extracting brain tissue (BET Mask) and then use FS6 for the remaining stages of the reconstruction.
While the final result of both constructions matches in most aspects, they don't occupy the same coordinates in space. Is there a way that we can match the coordinates of each voxel for two images? Or in other words make them compatible.
The Platform we use is CentOS7 .
Thanks and all the best, Ela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you so much. This actually worked well. Just two simple follow-up questions:
1. Do I assume right that this solution doesn't work on aparc+aseg? 2. If I want to run recon-all -autorecon2 -autorecon3 on a subject that I have a proper brain mask for (named brainmask.nii), can I simply run the command: 3. recon-all -autorecon2 -autorecon3 -i brainmask.nii -s <subjectid> ? or do I need more proper flags?
Thank you again.
Subject: Re: Recon-all reconstructed image coordinates
You can try registering them together like mri_coreg ---mov betmaskvolume.nii.gz --targ orig.mgz --reg reg.lta Then
mri_vol2vol --mov betmaskvol.nii.gz --targ orig.mgz --reg.lta --o betmask-in-fs.mgz --interp nearest The betmaskvol should be the intensity image (like orig.mgz) and not a binary mask or segmentation
________________________________ From: Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Wednesday, February 2, 2022 4:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: Recon-all reconstructed image coordinates
Hi all,
I just wanted to follow-up on this message with one extra piece of information added:
The two brains are exactly identical. Considering that we have two identical reconstructed brains (exactly the same as each other), with the only difference being that one of them is a little bit shifted and rotated in comparison to the other one, if there a way to measure the amount of this rotation and shift? If yes, can this information be used to counteract this rotation and shift? In other words, can we rotate and shift the second brain back in the exact opposite direction, so it completely overlays the first brain using freesurfer?
Thank you and all the best, Ela ________________________________ From: Salar Dini, Elaheh Sent: Monday, January 31, 2022 6:46 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Recon-all reconstructed image coordinates
Dear Freesurfer developers, In the link below, you see two brains belonging to the same subject:
https://secure-web.cisco.com/1H4mFA41ntCvRefEpinn6dBz0q4VleYSG1krhtaqGoWUHC-... [https://secure-web.cisco.com/1xznD5ZYOm35iKN3POq1qUehtO5guEXO3hECSfVb4FVboPQ...https://secure-web.cisco.com/1H4mFA41ntCvRefEpinn6dBz0q4VleYSG1krhtaqGoWUHC-bLIPQULQkxZ9-w1LHWd5L06000XQC35IIs1MdsqpZtSvq5PuTwOsGCUvX_K6BpkEFTRWy1sk3bvNhUkurdB64zeX-LToavxx1l1ty5m7v-U_DF2J0U850dnOKVT36r-UnSNqXrKPvachSJdLMYm9BX4I8TFcs3Uq2VtV4mdWngZoxWYBTDw669-y_Lzg_4VbOVHqvdQIomUU3MEKDK2a9P9rAjxelT9Y5y20mqWgr6FoTpeDLaQ5_rB95p2hb2RiPhUQCi486wwmgFCR3O9BBhayeGo0-9ZrHyxaD7yA/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0 Screen Shot 2022-01-26 at 1.40.23 PM.pnghttps://secure-web.cisco.com/1H4mFA41ntCvRefEpinn6dBz0q4VleYSG1krhtaqGoWUHC-bLIPQULQkxZ9-w1LHWd5L06000XQC35IIs1MdsqpZtSvq5PuTwOsGCUvX_K6BpkEFTRWy1sk3bvNhUkurdB64zeX-LToavxx1l1ty5m7v-U_DF2J0U850dnOKVT36r-UnSNqXrKPvachSJdLMYm9BX4I8TFcs3Uq2VtV4mdWngZoxWYBTDw669-y_Lzg_4VbOVHqvdQIomUU3MEKDK2a9P9rAjxelT9Y5y20mqWgr6FoTpeDLaQ5_rB95p2hb2RiPhUQCi486wwmgFCR3O9BBhayeGo0-9ZrHyxaD7yA/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0 Shared with Dropbox http://secure-web.cisco.com/16sBNoufrtEOz_3D9ZAKULgn51oWBta8bcp86BBRZDneGMxX...
while one of them is reconstructed with FS7.2, the other one is reconstructed with a pipeline that uses another code for extracting brain tissue (BET Mask) and then use FS6 for the remaining stages of the reconstruction.
While the final result of both constructions matches in most aspects, they don't occupy the same coordinates in space. Is there a way that we can match the coordinates of each voxel for two images? Or in other words make them compatible.
The Platform we use is CentOS7 .
Thanks and all the best, Ela
On 2/7/2022 5:29 PM, Salar Dini, Elaheh wrote:
External Email - Use Caution
Thank you so much. This actually worked well. Just two simple follow-up questions:
- Do I assume right that this solution doesn't work on aparc+aseg?
Correct, that will not work
If I want to run recon-all -autorecon2 -autorecon3 on a subject that I have a proper brain mask for (named brainmask.nii), can I simply run the command:
recon-all -autorecon2 -autorecon3 -i brainmask.nii -s <subjectid> ? or do I need more proper flags?
That might work. You can also run it up to where it creates the brainmask.mgz and just copy your file into over it and re-run
Thank you again.
*Subject:*Re: Recon-all reconstructed image coordinates You can try registering them together like mri_coreg ---mov betmaskvolume.nii.gz --targ orig.mgz --reg reg.lta Then mri_vol2vol --mov betmaskvol.nii.gz --targ orig.mgz --reg.lta --obetmask-in-fs.mgz --interp nearestThe betmaskvol should be the intensity image (like orig.mgz) and not abinary mask or segmentation
*From:* Salar Dini, Elaheh elaheh.salardini@yale.edu *Sent:* Wednesday, February 2, 2022 4:05 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: Recon-all reconstructed image coordinates Hi all,
I just wanted to follow-up on this message with one extra piece of information added:
The two brains are exactly identical. Considering that we have two identical reconstructed brains (exactly the same as each other), with the only difference being that one of them is a little bit shifted and rotated in comparison to the other one, if there a way to measure the amount of this rotation and shift? If yes, can this information be used to counteract this rotation and shift? In other words, can we rotate and shift the second brain back in the exact opposite direction, so it completely overlays the first brain using freesurfer?
Thank you and all the best, Ela
*From:* Salar Dini, Elaheh *Sent:* Monday, January 31, 2022 6:46 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Recon-all reconstructed image coordinates Dear Freesurfer developers, In the link below, you see two brains belonging to the same subject:
*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.dropbox.com/s/c2gsp8h8jj7c93d/Screen%20Shot%202022-01-26%20at%20... https://secure-web.cisco.com/1H4mFA41ntCvRefEpinn6dBz0q4VleYSG1krhtaqGoWUHC-bLIPQULQkxZ9-w1LHWd5L06000XQC35IIs1MdsqpZtSvq5PuTwOsGCUvX_K6BpkEFTRWy1sk3bvNhUkurdB64zeX-LToavxx1l1ty5m7v-U_DF2J0U850dnOKVT36r-UnSNqXrKPvachSJdLMYm9BX4I8TFcs3Uq2VtV4mdWngZoxWYBTDw669-y_Lzg_4VbOVHqvdQIomUU3MEKDK2a9P9rAjxelT9Y5y20mqWgr6FoTpeDLaQ5_rB95p2hb2RiPhUQCi486wwmgFCR3O9BBhayeGo0-9ZrHyxaD7yA/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0 https://secure-web.cisco.com/1H4mFA41ntCvRefEpinn6dBz0q4VleYSG1krhtaqGoWUHC-bLIPQULQkxZ9-w1LHWd5L06000XQC35IIs1MdsqpZtSvq5PuTwOsGCUvX_K6BpkEFTRWy1sk3bvNhUkurdB64zeX-LToavxx1l1ty5m7v-U_DF2J0U850dnOKVT36r-UnSNqXrKPvachSJdLMYm9BX4I8TFcs3Uq2VtV4mdWngZoxWYBTDw669-y_Lzg_4VbOVHqvdQIomUU3MEKDK2a9P9rAjxelT9Y5y20mqWgr6FoTpeDLaQ5_rB95p2hb2RiPhUQCi486wwmgFCR3O9BBhayeGo0-9ZrHyxaD7yA/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0
Screen Shot 2022-01-26 at 1.40.23 PM.png https://secure-web.cisco.com/1H4mFA41ntCvRefEpinn6dBz0q4VleYSG1krhtaqGoWUHC-bLIPQULQkxZ9-w1LHWd5L06000XQC35IIs1MdsqpZtSvq5PuTwOsGCUvX_K6BpkEFTRWy1sk3bvNhUkurdB64zeX-LToavxx1l1ty5m7v-U_DF2J0U850dnOKVT36r-UnSNqXrKPvachSJdLMYm9BX4I8TFcs3Uq2VtV4mdWngZoxWYBTDw669-y_Lzg_4VbOVHqvdQIomUU3MEKDK2a9P9rAjxelT9Y5y20mqWgr6FoTpeDLaQ5_rB95p2hb2RiPhUQCi486wwmgFCR3O9BBhayeGo0-9ZrHyxaD7yA/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0 Shared with Dropbox www.dropbox.com
while one of them is reconstructed with FS7.2, the other one is reconstructed with a pipeline that uses another code for extracting brain tissue (BET Mask) and then use FS6 for the remaining stages of the reconstruction.
While the final result of both constructions matches in most aspects, they don't occupy the same coordinates in space. Is there a way that we can match the coordinates of each voxel for two images? Or in other words make them compatible.
The Platform we use is CentOS7 .
Thanks and all the best, Ela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Salar Dini, Elaheh