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Hi! I am trying to make a ribbon.mgz from a non-human primate surface recon that does not have an aseg. Following this prior discussion: Re: [Freesurfer] ribbon.mgz Without aseg.mgz (mail-archive.com) https://secure-web.cisco.com/1ak2oe-adeCSsLNqdcSfpPz47btc0Bg4_-64m15yi4A3arakBiE7rQ-e9Ic--HcZjzBr8owRBFUicdouc7e2zl78qnX0T7FnwdllHDGAeM_4lAB6y3cenwxCzUG3lomlWl7BjXQbs4PesuZet8wvOXyZgrU9ePd4D9fZQEHvmpLBuI3G_a9NjVljMypuSefd0w8HYbmqeeqk3V6FQctpxtYq7VxlSRohysbd2HtGet4ulmKNUGr16_yWQ5tGzBFans_D-RTGtinwVa8sbtjRjqg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg21349.html I tried mri_ribbon:
mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz rh.ribbon.mgz
Attached is the output. It looks like it roughly follows the grey matter, but especially the sulci seem to be filled. Unfortunately, there is no help for mri_ribbon. Any advice on how to proceed? The above mentioned discussion did not lead to a conclusion on how to get a ribbon without aseg. Thank you! Caspar
Try cd yoursubjectname/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon yoursubjectname
On 5/3/2021 4:31 PM, Caspar M. Schwiedrzik wrote:
External Email - Use Caution
Hi! I am trying to make a ribbon.mgz from a non-human primate surface recon that does not have an aseg. Following this prior discussion: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* Re: [Freesurfer] ribbon.mgz Without aseg.mgz (mail-archive.com) https://secure-web.cisco.com/1ak2oe-adeCSsLNqdcSfpPz47btc0Bg4_-64m15yi4A3arakBiE7rQ-e9Ic--HcZjzBr8owRBFUicdouc7e2zl78qnX0T7FnwdllHDGAeM_4lAB6y3cenwxCzUG3lomlWl7BjXQbs4PesuZet8wvOXyZgrU9ePd4D9fZQEHvmpLBuI3G_a9NjVljMypuSefd0w8HYbmqeeqk3V6FQctpxtYq7VxlSRohysbd2HtGet4ulmKNUGr16_yWQ5tGzBFans_D-RTGtinwVa8sbtjRjqg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg21349.html I tried mri_ribbon: mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz rh.ribbon.mgz Attached is the output. It looks like it roughly follows the grey matter, but especially the sulci seem to be filled. Unfortunately, there is no help for mri_ribbon. Any advice on how to proceed? The above mentioned discussion did not lead to a conclusion on how to get a ribbon without aseg. Thank you! Caspar
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Hi Doug, Thank you - we tried this. We do not have aseg and therefore mris_volmask will not do it. Caspar
On Mon, May 10, 2021 at 18:09 Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Try cd yoursubjectname/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon yoursubjectname
On 5/3/2021 4:31 PM, Caspar M. Schwiedrzik wrote:
External Email - Use CautionHi! I am trying to make a ribbon.mgz from a non-human primate surface recon that does not have an aseg. Following this prior discussion: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* Re: [Freesurfer] ribbon.mgz Without aseg.mgz (mail-archive.com) https://secure-web.cisco.com/1VdhFmYoi68s4-hWpx9b4PfGpWUxkuRYYnXFCVuOciL9pr9mToywFyr2sqpYsJf65LEgYSj2hae4hAhYDMAB1jrUggSJWAytxF_88Z1j4Vz9TABX6c6YtM2b4eztak0ks45cDnxK237yA-5nOCA_oBbkEEN_wiSdupbhdIRKh06PnTvRTxsbF0Q42T3bPjecEYo88skGdbzWwu1s3FkEShAUCs4te0t0rtAoOpav5uVwzH1KK2aG-Llm18v6otSq2/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1ak2oe-2DadeCSsLNqdcSfpPz47btc0Bg4-5F-2D64m15yi4A3arakBiE7rQ-2De9Ic-2D-2DHcZjzBr8owRBFUicdouc7e2zl78qnX0T7FnwdllHDGAeM-5F4lAB6y3cenwxCzUG3lomlWl7BjXQbs4PesuZet8wvOXyZgrU9ePd4D9fZQEHvmpLBuI3G-5Fa9NjVljMypuSefd0w8HYbmqeeqk3V6FQctpxtYq7VxlSRohysbd2HtGet4ulmKNUGr16-5FyWQ5tGzBFans-5FD-2DRTGtinwVa8sbtjRjqg_https-253A-252F-252Fwww.mail-2Darchive.com-252Ffreesurfer-2540nmr.mgh.harvard.edu-252Fmsg21349.html%26d%3DDwMDaQ%26c%3DJeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg%26r%3DsgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8%26m%3D2KmDkufF0O3Q4E6ttVSwu3wsGnvInZisgxeLGFgrfuU%26s%3D9xoJKKfQdjJpr9qu9W-wNKDJMWGsyXvHbQb5CcWiPTk%26e%3D I tried mri_ribbon:
mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz rh.ribbon.mgz
Attached is the output. It looks like it roughly follows the grey matter, but especially the sulci seem to be filled. Unfortunately, there is no help for mri_ribbon. Any advice on how to proceed? The above mentioned discussion did not lead to a conclusion on how to get a ribbon without aseg. Thank you! Caspar
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1mz7WZrkRPDwrShMPb1tXkY-mRsPzMgKF-Q4b-h6l7SaGpfyv3sUC-yDH_vSKLPd3H97pWf88l9HXgwFlcczIxl1Ja7RV0Xn1mKVOwFOjcg4KzYHA_cDwPbLJBxDSLOlnA6hDqPD7blbQdBCJ_DyXq3HJVFjY5cqLIAFLRav6uxS_8osdDa77IRRJouXyUcXoW5cttKs87do4d2t1dxthG_f51WwPdJ8jYGMNVTifzIMmytDsEzVNxxxofL86rmPZ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwMDaQ%26c%3DJeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg%26r%3DsgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8%26m%3D2KmDkufF0O3Q4E6ttVSwu3wsGnvInZisgxeLGFgrfuU%26s%3DC1SiGScTdN8YSI2geBFcgLuWYDznWo129s3_BUD66Go%26e%3D
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You can try using mri_surf2vol. Run with --help and use method1
On 5/10/2021 12:54 PM, Caspar M. Schwiedrzik wrote:
External Email - Use Caution
Hi Doug, Thank you - we tried this. We do not have aseg and therefore mris_volmask will not do it. Caspar
On Mon, May 10, 2021 at 18:09 Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Try cd yoursubjectname/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon yoursubjectname On 5/3/2021 4:31 PM, Caspar M. Schwiedrzik wrote:External Email - Use Caution Hi! I am trying to make a ribbon.mgz from a non-human primate surface recon that does not have an aseg. Following this prior discussion: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* Re: [Freesurfer] ribbon.mgz Without aseg.mgz (mail-archive.com) <https://secure-web.cisco.com/1VdhFmYoi68s4-hWpx9b4PfGpWUxkuRYYnXFCVuOciL9pr9mToywFyr2sqpYsJf65LEgYSj2hae4hAhYDMAB1jrUggSJWAytxF_88Z1j4Vz9TABX6c6YtM2b4eztak0ks45cDnxK237yA-5nOCA_oBbkEEN_wiSdupbhdIRKh06PnTvRTxsbF0Q42T3bPjecEYo88skGdbzWwu1s3FkEShAUCs4te0t0rtAoOpav5uVwzH1KK2aG-Llm18v6otSq2/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1ak2oe-2DadeCSsLNqdcSfpPz47btc0Bg4-5F-2D64m15yi4A3arakBiE7rQ-2De9Ic-2D-2DHcZjzBr8owRBFUicdouc7e2zl78qnX0T7FnwdllHDGAeM-5F4lAB6y3cenwxCzUG3lomlWl7BjXQbs4PesuZet8wvOXyZgrU9ePd4D9fZQEHvmpLBuI3G-5Fa9NjVljMypuSefd0w8HYbmqeeqk3V6FQctpxtYq7VxlSRohysbd2HtGet4ulmKNUGr16-5FyWQ5tGzBFans-5FD-2DRTGtinwVa8sbtjRjqg_https-253A-252F-252Fwww.mail-2Darchive.com-252Ffreesurfer-2540nmr.mgh.harvard.edu-252Fmsg21349.html%26d%3DDwMDaQ%26c%3DJeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg%26r%3DsgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8%26m%3D2KmDkufF0O3Q4E6ttVSwu3wsGnvInZisgxeLGFgrfuU%26s%3D9xoJKKfQdjJpr9qu9W-wNKDJMWGsyXvHbQb5CcWiPTk%26e%3D> I tried mri_ribbon: mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz rh.ribbon.mgz Attached is the output. It looks like it roughly follows the grey matter, but especially the sulci seem to be filled. Unfortunately, there is no help for mri_ribbon. Any advice on how to proceed? The above mentioned discussion did not lead to a conclusion on how to get a ribbon without aseg. Thank you! 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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.
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Caspar M. Schwiedrzik -
Douglas N. Greve