for the annot, it should get the color table from the annot itself. for the output, there is not an option to change the colortable, but you can just mri_convert -ctab your.ctab file.mgz file.mgz
On 2/14/2022 3:49 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Is there an argument to put in a custom LUT? I don’t see it in the options for mri_surf2volseg. I’m assuming I have to put in average/colortable_vpnl.txt and average/colortable_BA.txt
Get Outlook for iOS
https://secure-web.cisco.com/1TolOmCVXnfUxV402Flx2lZ_4NgimOtRJ5HqRmB0MkHN3pv_zWs9OUBtwdc7aXycd_68LRgjoMWoK9eSC33B3ipLD24YreBbGWRfWjRtrN_XJc7PFc1wRamjc4_1OaaEdPfczupHcvTZnSUN0jvPhyuJKTfQxq30Epgqa0S8QJ9OE6oe--pByQMI21QOe8trJf6QZx1RtajhkCARbHScEwOVOZ4et5YFudxu-5ewtfG-NcJ0sfCDAKRWLEvTzyssh_qFrWiaXLR4mo8D-j_eMx345fvg_2BW40oMYCdeqgoElPrB1GMUgC7ZirCIpVLQF/https%3A%2F%2Faka.ms%2Fo0ukef
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Sunday, February 13, 2022 10:42:41 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] [External] Re: white matter measurements for labels/annotations You'll have to create an annotation first (maybe with mris_label2annot), then use mri_surf2volseg to create the segmentation. Look at the command line to create wmparc.mgz
On 2/4/2022 10:03 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Yes but instead of DKT regions, it would have brodmann area for example
Get Outlook for iOS
https://secure-web.cisco.com/1eAC_sZNKcMaGtet6rH2PGu5G4O6IM7T1xgyPg2lYkiuXiFocr6UaRrTBB2_ccJP-zaT8inBrpb90iVsK_zmleFo9alxcZti_f5NgVxAhV5LLjJzO6irIEBSRaxyclZIVpY_50y5rwTTEGXsYlXuFciCgroh_moa4qfm2jFNvDt1WC4idPTmL952Zlvb4zpLFXGhFCJVLU7KhQM5K99PUeyqbVLlDIGdWy-9ge9GBzOlBEgtQ6Q_g0rd6tlNn9ZCV86tNmIghaJcI4QkpBniukWOfeGk8Q-3Cm5RqhdeYzMDdABM0_rLCcz52fCV4nm7r/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1p6IJUtHw7r98MRJZmstZAvHtX_wW2AIUBNiE1Ru4Nl56H63etcrTRbrwjm6oMeMb-WurHyDiVOtflPhIal4sLy4qFOGC_doqsiEF-fitmdTOrl0QSvZrm9sUiVA7os-H0BRN_bxcPExO442M5gi_aPaqX5M1z5isB4u_sAa50FHkMZBAhm2wf47PZ8XajrsLRev2Uz1YiZfIi5k9ZcNMBOUmMNoYlsIPdP1kPpHOEblutnsmOOCxVPOveRk0Ba8C4JJgQYxhF1SbqdTbu3NPGmFzg84r5IsXt0ZwIrwiYBP1yC3hDN6sMdhfyCBg5T5ch-leaKBBZynU6kU0T4NFhg%2Fhttps%2A3A%2A2F%2A2Faka.ms%2A2Fo0ukef__%3BJSUlJQ%21%21CvMGjuU%21qQludDg84WHDNf1EPR3eTwQ9VILKgcy3wTRRING4QpnfGcmrvFbDuTPVe2A6WXdytd3a3w%24
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Friday, February 4, 2022 7:10:17 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] white matter measurements for labels/annotations Do you mean something like wmparc.mgz and wmparc.stats?
On 2/1/2022 1:10 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi,
is it possible to extract white matter volume estimations for labels/annotations? I am specifically wondering about the brodmann atlas and the stanford atlas that is already included in latest FS.
Thanks,
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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/1YlG-lqYueaGEe5ZxWguqptv7wJ4pPmVwiP0xAiNaSKyGtaXur33xcOjeJHRKNET6gmGWiY60147nIj-ZzCui7GZTJBXCbPWmHExsxDiBlHkZV1LdYS3aX0H5l2ZU8mRWpbMHxaxzLowfgPyFMK_Uc3M_P8JKtMhJLXfgtgfwH1mubnSp3Fc5Uk4xHMo0_mud2miWzs6hgUbRzT_KID-rR0kDemr-i986oAXLsLAx5ssE80y3NYVzBcu4AwBmzB9QB1hOUF0WRM_3vhSMU4miR2UcicuP95uHLSHg8TGeKR-XYdVladP8m4LvtRUQSjbI/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1yCJtbi5aEUr7ZP40voUIHZ36iC_RpgPWEOrHQUwG_rUPS2kOYdT1GMy_uUXthm5haeQjle8D9VJUhlXGWd29KGLucyRjA3BumbKBi-qdrzwzlbe0tATDYSEwjWEkTlmeLlN3ux4HrwRHE0eACOoK7T-AgMLKKRgfgWi4s55C95n2bWjmvMRsdBZE1qAtgaBXil9UjvNxciFnnLMQsofFFC2TA0mTpRnIy0vzUAZOLng8HqV90QBLhXp98LiFd1ADJ71uV30GHuAsHLx0icMeNwmEDH_upVHw4M23Iz3WPLJBY85lMzTV_05FJ2-e9LpI9NfKPEqcnKq749AdDo4hbw%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2F%2A2Fmail.nmr.mgh.harvard.edu%2A2Fmailman%2A2Flistinfo%2A2Ffreesurfer__%2A3B%2A21%2A21CvMGjuU%2A21pdc13KZgGqsADpUQ2yIsfk5QZ33ib4fRxrOB_MbxlJ0Wmt2SKZgpKdJdGks-mmfepMk88A%2A24__%3BJSUlJSUlJSUlJSUlJSUlJQ%21%21CvMGjuU%21qQludDg84WHDNf1EPR3eTwQ9VILKgcy3wTRRING4QpnfGcmrvFbDuTPVe2A6WXdk6SZquA%24
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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/1Nm7ycz4ePPAqS6pHcOuYxq4fk5-ocwB-9XU9S-UEDWerNDpzJRF48cn33FlHxpZxFuga3JpYRFGxXcpksj14PiZuSdUt3ZwuaIkQ4psALxTToWdEcLyzkKMTMuH5jd0sL824xLMq4ehRVCgFuvztwArTMDA5_7nv1wlMJJ_pZ17NqwLnw8Z3oeCg0058mfTiMHI2uUmP3mvkh3Jacw9wJFHIhPTJ0R8FvgelxWSh5m03KeDE8-kB3hE5xi4UwjaoS7v-6apcqzmSevI4CHkTgA0S7lCJnTp96h1AdYTcXTo4cmwBiv3Ca1dPYHVjLeeD/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21CvMGjuU%21qQludDg84WHDNf1EPR3eTwQ9VILKgcy3wTRRING4QpnfGcmrvFbDuTPVe2A6WXdXFkzlGA%24
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer