Re: [Freesurfer] how to shrink WM surface in one region
External Email - Use Caution Hi Bruce, Thanks for the quick reply. I'm unable to connect to the ftp or file drop sites outlined here: https://secure-web.cisco.com/1J6xj9uOYT0-orYt6Ug7tMaMV01I_XctGV48pcqQv9Tr9ubNryoR2olV4-GZJyFgXWIBKzChaTvUZ54ksRY3KJN7HS48GCFQHRgDcmX_C-9ExNQIhqWdtNsYPC5OXH5nhrGcAKr3-uf272_69Veym_yD9lSwnLGQPUn5WQu9064ju2XzAwLDCebCC96F4Y6omecL5RtQ1JZSrfRCQEzghed-QmdPB_hYiSPIEAr2WmeST-j61bq6MsltUPilNv1Zb3m64BXbT7ODVQNFrmgDgaw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFtpFileExchange. I can log into the ftp server, but don't have permissions access to drop files there. ...So instead, I put the image snapshots in a public google doc here: https://secure-web.cisco.com/183XTP5FLjT6Xx2SHQPem_2YqmbLW8bRZYSzfF6XOXFaE26dUdAVup5y7KygrjHrik6wX5NA-RoUFJlfQWQ1z4451Xv53-Xvt5JoaARbOpbtSWgIiJ6USMmPPiJchKK87-3qYOBDqU0FBAceHoAVuxP0igy5Wq9ElrROrkaUFodEjCvo8v7aiYduMuVx5Wp82JZbB2XkL8bAOZCJmFHibVCc0czcug4fUNasmddKRZMghDLeyqaPiWWculL5jw8L6HZ2RiZNWPoeRFvbyO3orYw/https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1HF5qcbiYRDdGZbvhoImfwVqX4xARgSnPDUnbuPKqMpY%2Fedit%3Fusp%3Dsharing Hopefully that will suffice. Thanks again, Lara From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Fischl, Bruce Sent: Wednesday, June 23, 2021 4:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to shrink WM surface in one region Hi Lara Can you send us some pictures? The answer depends on why the white matter surface is settling at the wrong place Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Lara Foland-Ross Sent: Wednesday, June 23, 2021 7:11 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] how to shrink WM surface in one region External Email - Use Caution Hi everyone, Very quick question - I need to shrink the white matter surface in a very specific (constrained) region. Can you please confirm that the right way to go about this is to (1) manually remove voxels from the WM volume in freeview, then (2) save edits on that WM volume, and then (3) run recon-all? Specifically, re: #3 - many brains also need control points, so I'm running " recon-all -autorecon2-cp -autorecon3" Using this command structure, I'm not seeing that any of the edits I'm making to the WM volume are influencing the white matter surface line... Only the control points. Thank you in advance, Lara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ol1Q11CaB9oKoj5iyxZnro7EGji1hj3xI4MFL1Hsy2IZrVINTJPmbPvZcM-KbzaSLERzuSaNvz-zO_GCUTwEG16g0DFEo4CDD6J34ArWooG7jtaD7QNeY4aL6fQf_uScApuPZB2prcI4tL4GnBthy74-WdVyT4PNgXOQ0jF6yNj83nGzNRCvgJMk8bYTYH-NIQALK_-K_3iT6RIdIQREAdwGWSNMtPKiUV831dKp0vWIw4F77ef35ftwu64z2Ke4X7xaU5na1TPQndcS5GCAjg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ol1Q11CaB9oKoj5iyxZnro7EGji1hj3xI4MFL1Hsy2IZrVINTJPmbPvZcM-KbzaSLERzuSaNvz-zO_GCUTwEG16g0DFEo4CDD6J34ArWooG7jtaD7QNeY4aL6fQf_uScApuPZB2prcI4tL4GnBthy74-WdVyT4PNgXOQ0jF6yNj83nGzNRCvgJMk8bYTYH-NIQALK_-K_3iT6RIdIQREAdwGWSNMtPKiUV831dKp0vWIw4F77ef35ftwu64z2Ke4X7xaU5na1TPQndcS5GCAjg/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 http://secure-web.cisco.com/1fzTQRYqmAV-6Yr9bfT3PR24391lt59doFpNwJpSwP1GhxfjWtTnxI6DTMZ66OOJw3lWjK2LAaSA2-MvNEb2-ZvkLDwUEDpf3bZ4d_nQ0iZPcZZ4f8EyY1EAhKTtyBQwHRIMMFMyxovr3mvsabMMS9QLgMgvMvoC1-auPiEGYuBwXKndZ7TYOL0E0JFWN64KYodiT183Z82J-kRdQq1Yko3k7APRzmKIOcol5rBovzffe5MvABb5IehdA2FkjoqhYCrFpt8QkXzIb4EZtCFfnUQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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
Re: [Freesurfer] how to shrink WM surface in one region
Hi Lara Can you send us some pictures? The answer depends on why the white matter surface is settling at the wrong place Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Lara Foland-Ross Sent: Wednesday, June 23, 2021 7:11 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] how to shrink WM surface in one region External Email - Use Caution Hi everyone, Very quick question - I need to shrink the white matter surface in a very specific (constrained) region. Can you please confirm that the right way to go about this is to (1) manually remove voxels from the WM volume in freeview, then (2) save edits on that WM volume, and then (3) run recon-all? Specifically, re: #3 - many brains also need control points, so I'm running " recon-all -autorecon2-cp -autorecon3" Using this command structure, I'm not seeing that any of the edits I'm making to the WM volume are influencing the white matter surface line... Only the control points. Thank you in advance, Lara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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] how to shrink WM surface in one region
External Email - Use Caution Hi everyone, Very quick question - I need to shrink the white matter surface in a very specific (constrained) region. Can you please confirm that the right way to go about this is to (1) manually remove voxels from the WM volume in freeview, then (2) save edits on that WM volume, and then (3) run recon-all? Specifically, re: #3 - many brains also need control points, so I'm running " recon-all -autorecon2-cp -autorecon3" Using this command structure, I'm not seeing that any of the edits I'm making to the WM volume are influencing the white matter surface line... Only the control points. Thank you in advance, Lara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to shrink wm surface
Hi Mike sorry, I never really documented it. Essentially they provide limits on the allowable intensities of the various tissue classes at the different boundaries (gray/white and pial). Unless those constraints are satisfied it will not try to place the boundary in that region cheers Bruce On Sat, 13 Sep 2014, Matt Glasser wrote: Have a look at mris_make_surfaces.c, this is how I learned about most of this stuff as the code is pretty well commented (and Bruce telling me things). Peace, Matt. On 9/12/14, 11:01 PM, Harms, Michael mha...@wustl.edu wrote: Hi Bruce, I was wondering if there is info somewhere about what each of those 7 MIN_ and MAX_ variables control regarding the positioning of the white and pial surfaces? thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 9/9/14 7:35 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Andrea what is the background image? This is usually either a failure of the intensity normalization or of the surface deformation/segmentation to adaptively estimate the underlying intensity distributions of the gray/white matter. If you look in recon-all.log for that subject you will find a set of lines like: setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 59.1 (was 40) setting MAX_GRAY to 100.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40) in your case for example you will probably find that the min_border_white is too high or tha the max_gray is too low. You can set these using the expert opts for both mri_segment and mris_make_surfaces. cheers Bruce On Tue, 9 Sep 2014, Andrea Horváth wrote: Dear Freesurfers, After running recon-all, the wm surfaces are too close to the pial surface, some gray matter is segmented as white matter as seen in the attached picture (red cross: a bigger cortical part is included in the white matter). How can I shrink the wm surface? Thank you for your help! Andrea The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to shrink wm surface
Hi Bruce, I was wondering if there is info somewhere about what each of those 7 MIN_ and MAX_ variables control regarding the positioning of the white and pial surfaces? thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 9/9/14 7:35 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Andrea what is the background image? This is usually either a failure of the intensity normalization or of the surface deformation/segmentation to adaptively estimate the underlying intensity distributions of the gray/white matter. If you look in recon-all.log for that subject you will find a set of lines like: setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 59.1 (was 40) setting MAX_GRAY to 100.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40) in your case for example you will probably find that the min_border_white is too high or tha the max_gray is too low. You can set these using the expert opts for both mri_segment and mris_make_surfaces. cheers Bruce On Tue, 9 Sep 2014, Andrea Horváth wrote: Dear Freesurfers, After running recon-all, the wm surfaces are too close to the pial surface, some gray matter is segmented as white matter as seen in the attached picture (red cross: a bigger cortical part is included in the white matter). How can I shrink the wm surface? Thank you for your help! Andrea The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to shrink wm surface
Have a look at mris_make_surfaces.c, this is how I learned about most of this stuff as the code is pretty well commented (and Bruce telling me things). Peace, Matt. On 9/12/14, 11:01 PM, Harms, Michael mha...@wustl.edu wrote: Hi Bruce, I was wondering if there is info somewhere about what each of those 7 MIN_ and MAX_ variables control regarding the positioning of the white and pial surfaces? thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 9/9/14 7:35 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Andrea what is the background image? This is usually either a failure of the intensity normalization or of the surface deformation/segmentation to adaptively estimate the underlying intensity distributions of the gray/white matter. If you look in recon-all.log for that subject you will find a set of lines like: setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 59.1 (was 40) setting MAX_GRAY to 100.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40) in your case for example you will probably find that the min_border_white is too high or tha the max_gray is too low. You can set these using the expert opts for both mri_segment and mris_make_surfaces. cheers Bruce On Tue, 9 Sep 2014, Andrea Horváth wrote: Dear Freesurfers, After running recon-all, the wm surfaces are too close to the pial surface, some gray matter is segmented as white matter as seen in the attached picture (red cross: a bigger cortical part is included in the white matter). How can I shrink the wm surface? Thank you for your help! Andrea The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to shrink wm surface
Dear Freesurfers, After running recon-all, the wm surfaces are too close to the pial surface, some gray matter is segmented as white matter as seen in the attached picture (red cross: a bigger cortical part is included in the white matter). How can I shrink the wm surface? Thank you for your help! Andrea ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to shrink wm surface
mris_expand may do what you want. You can use it to shrink or expand the points on a surface by a fixed percentage or a fixed distance. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Andrea Horváth Sent: Tuesday, September 09, 2014 7:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] how to shrink wm surface Dear Freesurfers, After running recon-all, the wm surfaces are too close to the pial surface, some gray matter is segmented as white matter as seen in the attached picture (red cross: a bigger cortical part is included in the white matter). How can I shrink the wm surface? Thank you for your help! Andrea ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to shrink wm surface
Hi Andrea what is the background image? This is usually either a failure of the intensity normalization or of the surface deformation/segmentation to adaptively estimate the underlying intensity distributions of the gray/white matter. If you look in recon-all.log for that subject you will find a set of lines like: setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 59.1 (was 40) setting MAX_GRAY to 100.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40) in your case for example you will probably find that the min_border_white is too high or tha the max_gray is too low. You can set these using the expert opts for both mri_segment and mris_make_surfaces. cheers Bruce On Tue, 9 Sep 2014, Andrea Horváth wrote: Dear Freesurfers, After running recon-all, the wm surfaces are too close to the pial surface, some gray matter is segmented as white matter as seen in the attached picture (red cross: a bigger cortical part is included in the white matter). How can I shrink the wm surface? Thank you for your help! Andrea ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
