Re: [Freesurfer] Cortical thickness difference as vertex-label overlay
External Email - Use Caution that seems to work. Thank you! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Sunday, September 12, 2021 11:23:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cortical thickness difference as vertex-label overlay Try mri_mask yourcontrast/gamma.mgh sig.masked.mgh yourcontrast/gamma.masked.mgh gamma is the contrast value (eg, patients minus controls). Is that what you wnat? On 9/10/2021 6:20 AM, Graterol Pérez, José Alberto wrote: External Email - Use Caution Hello, I've done a group comparison between patients and controls, and obtained some significant cortical thickness (CT) clusters. Is there a way to obtain an overlay similar to the sig.masked, but for the vertex-wise CT values instead of the p values? Best José Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1hAzh1jBu63H6tVGgotsuavQ6dsaNlwpucUWJaC6PJmxRj9XTKj82C0c6kVpY7No9DtPZFbS5n_iGOItG_ePjJFxELxCJpsMNPIHWycX6YqT0gDanbd8DLUb1X6YfoMVgiZYPwCv7TghXJdkxTg8NS-hnF3uW4MXfkmU0ynpDULO1WWWhua71aukdjHxJXKuhtGmwxdnbtG7_o40QX3K2fXeI39wnRPqMLRDYzQDOrJ3CrZ0_QCWG-6Qr_eJencEWagoT7lj2KNi30MsR2zvi5g/http%3A%2F%2Fwww.uke.de<http://secure-web.cisco.com/1e7AftRvFI-NEMfuT18S0RBQu0b88KQG6OyJdlKgcz5IMkhd75fpD7-o-WzjqBZzIv-7OEK5u0xsv4O-Mw1pwO_NB9017Grf5V1CPlyv_hMP3GSs9XgikNYhIoJV-a9DvEXBB1B9Yvr8P9GIpHq-d15RJgqxsgVpzx92WEBPyW-cnCKGLPLFmjeKYvLZbHmsJb-k_EBHmRmH90VxNfN7b1ZE1Ui0MAN4AESRVX1iAzlgnDicuwallRoUov_1uDu3CxOxcjduQCDMV4drLFgydNQ/http%3A%2F%2Fwww.uke.de%2F> Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel SAVE PAPER - THINK BEFORE PRINTING ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/19mGTQRUU9Ej5uctZW1_qg-gBpnqzdazL7mpH0vD7xSjWdaV36pgsfo7AAX46lmk8jLtdoVZbN3PgyH0-ZoXy9GzN8n4-1vsix3DpVMO5GpsJEIhaTw4fo01ux9xhfz7HhWDfLruPfxVmxPk636blvRZKqo0GwAaif-Mq4-ze6JuR3tMaTJ_fZW01mAXl55sq7qcJZbRinuEmgvrtKKxAiCk-UMyRwQXQXcvmnf36_A4wF85YqggK5mHq2UsXvgTY6pt6XrLVKXhqsBpVLK3O3w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer -- _ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/1hAzh1jBu63H6tVGgotsuavQ6dsaNlwpucUWJaC6PJmxRj9XTKj82C0c6kVpY7No9DtPZFbS5n_iGOItG_ePjJFxELxCJpsMNPIHWycX6YqT0gDanbd8DLUb1X6YfoMVgiZYPwCv7TghXJdkxTg8NS-hnF3uW4MXfkmU0ynpDULO1WWWhua71aukdjHxJXKuhtGmwxdnbtG7_o40QX3K2fXeI39wnRPqMLRDYzQDOrJ3CrZ0_QCWG-6Qr_eJencEWagoT7lj2KNi30MsR2zvi5g/http%3A%2F%2Fwww.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _ SAVE PAPER - THINK BEFORE PRINTING ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cortical thickness difference as vertex-label overlay
External Email - Use Caution Hello, I've done a group comparison between patients and controls, and obtained some significant cortical thickness (CT) clusters. Is there a way to obtain an overlay similar to the sig.masked, but for the vertex-wise CT values instead of the p values? Best José -- _ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/1-wFjFF0QdKwKy2LqouXvxJzgHC1mBAGCrGfRZL2KCrD7zAFUdiAEOKLcbYlmVtMpD-NeN6gYjKkE_E2YUWJf22oSCmlX0MpCqFKKh9auUczlEOHzjSKvJ_zs_w_4r6rixpKBBoB8nPLSpa2M0cO4eGszLYL5LwEDy36aYeBXJCC6S1ThGoCbfc23Z7Fju6zloeY58708_uNSoZNQwZdDp_NwZmyVv8QQugOcEyuQ-zb3Od0VvFh3iBbzHCDOe32hITQq0qSmxW6C2cRgBlFAcw/http%3A%2F%2Fwww.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _ SAVE PAPER - THINK BEFORE PRINTING ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] White matter parcellation
External Email - Use Caution Hey, Douglas. Thanks for the answer and the references. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Tuesday, February 2, 2021 5:57:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter parcellation The subcortical GM structures are obtained from the whole brain segmentation (Fischl, Neuron, 2002). The segmentation of the WM is performed by taking the label of the closest point on cortex (Salat, Neuroimage, 2009) On 2/1/2021 1:52 PM, Graterol Pérez, José Alberto wrote: External Email - Use Caution Dear FreeSurfer experts, I need help trying to understand how the white matter gets parcellated. I have a clinical dataset, which means that the resolution is not as research images, but it ran without a problem. I would like to measure the volume of the basal ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a structure ends and the other one begins. I am attaching two images to show what I mean. I would really appreciate some clarification. I am using FreeSurfer 7.1.1 Thanks in advance. José Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1YDQZYR7S2qJ4SG_NP8gFjH9ioGs9qVAJxK-GZmNW_gbT-5QUHxrPVTP5xn6UlBVqY2nW9sNQoU_345O7oDQRFm-dDi-dy9IzEObVr4RfJSSzHB0NV3vRHUgEX3Ya_v91P3TocbisuE1fxWi6ylHkc4Sxw3nITfA6n0Jg48C7r7piC4mWkEc_jKqDqkd6PlNgMUYrg0Abs4vKQu3d-jUm28pAgPgYc2Zv267P4xpxG1Mf-BshlKiS9l9uOywQVE0PzeF1FdHBzsmA7-yuSwey_g/http%3A%2F%2Fwww.uke.de<http://secure-web.cisco.com/1TNVlubeEY5RNf4oFHEY5w6gheVEoD4jo9r88zJkPdQ2aOlEQFLWA3ibkhLFQcnM5_K8aBICfUSAq-8vUUHSj-xx2Vssd8w4kXgyf1amgqCTReB780TWu7lTvgcJntfpA-NotaYQz5TDAwpgmUIokpu_mXWyeM1jlwQ5Mt4RYFFQLFUb_dEmXzRqtkPJp7ZaRkGuLZBW01AVPtbv2ULmyM2a6i7CmNrErvQm2kSdAYSiBlMnh2el8dO3zsqImHAkYAjLWT5S4-kKynzWM1352EQ/http%3A%2F%2Fwww.uke.de%2F> Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel SAVE PAPER - THINK BEFORE PRINTING ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1zRhx4neXfxE6wjV2715n3qDQ0xa_CZIon5Iy-aK56jikSZh2JQJD8lhdUfOe5CEWNKo2-3Xg4lsIrHHQKcNDrpDPiJIEFBM06sBzYCoSo9BlKFLDVlXzbF-bXVWWWXNPOYpXnOj8SC779lmp0R_XuNzL8g3h_k0pmdtk1qf5WW1yBp4thc9zEyLQh_Yn78V0YgvzrVf3oyBNWYYutAbvlm9k56eO16k6T9S0nJ4QL8pkIdoPmOMlCLROER7xqsxBbgWVGnREEBrr1Q6gxnew_w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer -- _ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/1YDQZYR7S2qJ4SG_NP8gFjH9ioGs9qVAJxK-GZmNW_gbT-5QUHxrPVTP5xn6UlBVqY2nW9sNQoU_345O7oDQRFm-dDi-dy9IzEObVr4RfJSSzHB0NV3vRHUgEX3Ya_v91P3TocbisuE1fxWi6ylHkc4Sxw3nITfA6n0Jg48C7r7piC4mWkEc_jKqDqkd6PlNgMUYrg0Abs4vKQu3d-jUm28pAgPgYc2Zv267P4xpxG1Mf-BshlKiS9l9uOywQVE0PzeF1FdHBzsmA7-yuSwey_g/http%3A%2F%2Fwww.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _ SAVE PAPER - THINK BEFORE PRINTING ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] White matter Parcellation
External Email - Use Caution Dear FreeSurfer experts, I need help trying to understand how the white matter gets parcellated. I have a clinical dataset, which means that the resolution is not as research images, but it ran without a problem. I would like to measure the volume of the basal ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a structure ends and the other one begins, because the structures are not really visible. I could upload two screenshots to show what I mean. I would really appreciate some clarification. I am using FreeSurfer 7.1.1 Thanks in advance. José -- _ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/1fL7_mV1HnVXx_pK-xzWgX0hp1IPRmxfnHHvyPV6axEvIN99tKLL4rqVW9pToIfDKy-D5Sm_-qItiTvmXlbn20AApfGepiSNRG9HD4nVqJXgD2cpm1eNEqG4CGCFXEMMHwAWOIZcxSELKpiTvtfJQqS11pDN-V6wawnKdKEd7q709fQspMZAmdsiRbiCBZeGtu7JWmdef5KX1_1XQUkedRDCAP2g8fHkjXOPFtXvENEUlMlNELzQjB3No_u-xwYGRwzkYNZorfNaylUj_2e3WKw/http%3A%2F%2Fwww.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _ SAVE PAPER - THINK BEFORE PRINTING ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
