External Email - Use Caution
Dear authors, I'm trying to reconstruct a model of a brain from an MRI, and after completion of recon-all (without any errors) the results are truly poor. By looking through your tutorials I am quite confident to say that the problem is either one of intensity normalisation or of white matter segmentation (possibly, both), as you can see in the images attached.
My first attempt is to insert some control points, though I wonder if I might need instead to fix the segmentation with the brush tool. Could it be possible to receive some feedback about this issue?
Another issue regards the freeview software, as whenever I move with the arrows from a slice to another the loaded surfaces suddenly disappear and won't reappear unless I delete and reopen them, and it makes it really hard to insert control points if I can't see the surfaces' outlines. Also, I was wondering if the computational cost of the autorecon2-cp is dependent significantly on the number of control points.
The pictures shows the lh.white, rh.white files over the T1.mgz file and the wm.mgz and control.dat files over the brain mask.mgz file.
Thanks in advance for your help, Tommaso Mariani
Hard to say from those images. In the 2nd, the surface is no where near where it should be -- it looks like it is misregistered with respect to the brain (that not an intensity problem). What is your freeview command to view the images?
On 12/23/2024 8:17 AM, Tommaso Mariani wrote:
External Email - Use Caution
Dear authors, I'm trying to reconstruct a model of a brain from an MRI, and after completion of recon-all (without any errors) the results are truly poor. By looking through your tutorials I am quite confident to say that the problem is either one of intensity normalisation or of white matter segmentation (possibly, both), as you can see in the images attached.
My first attempt is to insert some control points, though I wonder if I might need instead to fix the segmentation with the brush tool. Could it be possible to receive some feedback about this issue?
Another issue regards the freeview software, as whenever I move with the arrows from a slice to another the loaded surfaces suddenly disappear and won't reappear unless I delete and reopen them, and it makes it really hard to insert control points if I can't see the surfaces' outlines. Also, I was wondering if the computational cost of the autorecon2-cp is dependent significantly on the number of control points.
The pictures shows the lh.white, rh.white files over the T1.mgz file and the wm.mgz and control.dat files over the brain mask.mgz file.
Thanks in advance for your help, Tommaso Mariani
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I tried to open them from the console, but it gave me some errors about the directory, so I opened them from the ribbon menu command "load surface". Another uncommon thing is that, after loading the surfaces, it gives me an error about the reconstruction of the inverse matrix...
Il Mer 1 Gen 2025, 23:28 Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
Hard to say from those images. In the 2nd, the surface is no where near where it should be -- it looks like it is misregistered with respect to the brain (that not an intensity problem). What is your freeview command to view the images?
On 12/23/2024 8:17 AM, Tommaso Mariani wrote:
External Email - Use CautionDear authors, I'm trying to reconstruct a model of a brain from an MRI, and after completion of recon-all (without any errors) the results are truly poor. By looking through your tutorials I am quite confident to say that the problem is either one of intensity normalisation or of white matter segmentation (possibly, both), as you can see in the images attached.
My first attempt is to insert some control points, though I wonder if I might need instead to fix the segmentation with the brush tool. Could it be possible to receive some feedback about this issue?
Another issue regards the freeview software, as whenever I move with the arrows from a slice to another the loaded surfaces suddenly disappear and won't reappear unless I delete and reopen them, and it makes it really hard to insert control points if I can't see the surfaces' outlines. Also, I was wondering if the computational cost of the autorecon2-cp is dependent significantly on the number of control points.
The pictures shows the lh.white, rh.white files over the T1.mgz file and the wm.mgz and control.dat files over the brain mask.mgz file.
Thanks in advance for your help, Tommaso Mariani
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1k0j7PTPgkFa5Rt3hHnWcOYX6LGx85txOld-VqW2Qvs5xm8... 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/1J__kxbquTUD8fzzFE4jPNQ7u7iT6vuxlOc7mdLFF-n_ZNm... < https://secure-web.cisco.com/1J__kxbquTUD8fzzFE4jPNQ7u7iT6vuxlOc7mdLFF-n_ZNm... . 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.
Try something like tkmeditfv subject nu.mgz -surfs
On 1/2/2025 4:50 AM, Tommaso Mariani wrote:
External Email - Use Caution
I tried to open them from the console, but it gave me some errors about the directory, so I opened them from the ribbon menu command "load surface". Another uncommon thing is that, after loading the surfaces, it gives me an error about the reconstruction of the inverse matrix...
Il Mer 1 Gen 2025, 23:28 Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
Hard to say from those images. In the 2nd, the surface is no where near where it should be -- it looks like it is misregistered with respect to the brain (that not an intensity problem). What is your freeview command to view the images? On 12/23/2024 8:17 AM, Tommaso Mariani wrote:External Email - Use Caution Dear authors, I'm trying to reconstruct a model of a brain from an MRI, and after completion of recon-all (without any errors) the results are truly poor. By looking through your tutorials I am quite confident to say that the problem is either one of intensity normalisation or of white matter segmentation (possibly, both), as you can see in the images attached. My first attempt is to insert some control points, though I wonder if I might need instead to fix the segmentation with the brush tool. Could it be possible to receive some feedback about this issue? Another issue regards the freeview software, as whenever I move with the arrows from a slice to another the loaded surfaces suddenly disappear and won't reappear unless I delete and reopen them, and it makes it really hard to insert control points if I can't see the surfaces' outlines. Also, I was wondering if the computational cost of the autorecon2-cp is dependent significantly on the number of control points. The pictures shows the lh.white, rh.white files over the T1.mgz file and the wm.mgz and control.dat files over the brain mask.mgz file. Thanks in advance for your help, Tommaso Mariani _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1k0j7PTPgkFa5Rt3hHnWcOYX6LGx85txOld-VqW2Qvs5xm8qQdRspHkemSu7VwAtiIqQBbtd6eRaSj34ORpwUduuxSvsQNskkOaERv2Bt0ojwi7qzkN4rVNAL-bp4WGJG8Zd0yGtsHmNOap4QnNhjZQQqYOMmVidPXP9CHUCqMel3dsBowKlJi4zE60Rdgi1Whqd0zhtubj_fCBFqnBd7Q9uT-8Ku34SuZzxYzKWnz9EVGyWONNG7qmOI7CtGdz9_CpePGKOFrlwmUgBcI763PcugZfuJLs5UvyKeUkY-kg2shoVsQa0D8zPZjaAbCLc4MNWNca-xodJFwbbzfZ2SEw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1k0j7PTPgkFa5Rt3hHnWcOYX6LGx85txOld-VqW2Qvs5xm8qQdRspHkemSu7VwAtiIqQBbtd6eRaSj34ORpwUduuxSvsQNskkOaERv2Bt0ojwi7qzkN4rVNAL-bp4WGJG8Zd0yGtsHmNOap4QnNhjZQQqYOMmVidPXP9CHUCqMel3dsBowKlJi4zE60Rdgi1Whqd0zhtubj_fCBFqnBd7Q9uT-8Ku34SuZzxYzKWnz9EVGyWONNG7qmOI7CtGdz9_CpePGKOFrlwmUgBcI763PcugZfuJLs5UvyKeUkY-kg2shoVsQa0D8zPZjaAbCLc4MNWNca-xodJFwbbzfZ2SEw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1J__kxbquTUD8fzzFE4jPNQ7u7iT6vuxlOc7mdLFF-n_ZNmpcjoBM1VMFccXK4EYQU9e_aHiArLvWetqzIfcsneb53wec2V224X0P6uf-INk_Rncp-4wElshAf0eKzN-Ttbj4LaQVaEUH4CmnCmQJ_1FIJUPi_vkHnRK8PNFo3P6W73DpEm6Bd48sHc_L9o-Wbnx5akPFJj3aDxMsj_aHQtwdV-F13w2YpXA6lkhO6M-_SVNkLVSHM-8eQeoenWLfWgQNuhS2GLLL7meaVnnV1iVE6k-wAkfkuQIt3zOoB3aum_uJI39cLE_0ASWDdmDY/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1J__kxbquTUD8fzzFE4jPNQ7u7iT6vuxlOc7mdLFF-n_ZNmpcjoBM1VMFccXK4EYQU9e_aHiArLvWetqzIfcsneb53wec2V224X0P6uf-INk_Rncp-4wElshAf0eKzN-Ttbj4LaQVaEUH4CmnCmQJ_1FIJUPi_vkHnRK8PNFo3P6W73DpEm6Bd48sHc_L9o-Wbnx5akPFJj3aDxMsj_aHQtwdV-F13w2YpXA6lkhO6M-_SVNkLVSHM-8eQeoenWLfWgQNuhS2GLLL7meaVnnV1iVE6k-wAkfkuQIt3zOoB3aum_uJI39cLE_0ASWDdmDY/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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Tommaso Mariani