External Email - Use Caution Thank you very much!
On Wed., Feb. 10, 2021, 10:05 a.m. Douglas N. Greve, <dgr...@mgh.harvard.edu> wrote: > Use mris_anatomical_stats to create an LUT with the -c option. You can > look in recon-all.cmd for an example. You only need to do one hemi as they > both will be the same. > There are four sections of the new LUT: lh cortex, rh cortex, lh WM, and > rh WM. For each one, you replicate the LUT created above but change the > index number (first column) by adding a constant: 1000, 2000, 3000, 4000. > You can also change the name to indicate the hemi and tissue type. Look in > $FREESURFER_HOME/FreeSurferColorLUT.txt > for how it works for the aparc+aseg.mgz and the wmparc.mgz. You can embed > the LUT in the file itself with > mri_convert file.mgz --ctab yournewLUT file.mgz > > > > On 2/9/2021 5:30 PM, Vinny K wrote: > > External Email - Use Caution > Thanks Doug, the commands gave the expected outputs. I used the original > lh and rh BA_exvivo annotations and got the new BA+aseg.mgz and wmBA.mgz > files. Yes, please let me know how to proceed with the new LUT. > > > > > > On Tue, Feb 9, 2021 at 10:47 AM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> Look in the subject/scripts/recon-all.cmd file of one of your subjects. >> You will find five mri_surf2volseg commands >> Use the 2nd one (the one that creates aparc+aseg.mgz) as your template >> and modify it to take your BA annotation and output a "BA+aseg.mgz" >> Use the last one ( the one that creates wmparc.mgz) as your template to >> create your new wmBA.mgz file, modifying it as needed. >> You will need to create a new LUT, but let's do that when you get there >> >> On 2/9/2021 10:26 AM, Vinny K wrote: >> >> External Email - Use Caution >> I am using freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 >> >> On Tue, Feb 9, 2021 at 9:55 AM Douglas N. Greve <dgr...@mgh.harvard.edu> >> wrote: >> >>> which version of FS are you using? >>> >>> On 2/5/2021 10:02 PM, Vinny K wrote: >>> >>> External Email - Use Caution >>> Hello, >>> >>> I'd like to obtain white matter parcellations of the Brodmann areas. I >>> am not certain that the generated wmparc file from recon-all has this type >>> of parcellation. I was able to convert Brodmann area label files to mgz >>> format using mris_label2annot and mri_aparc2aseg commands. How can I >>> obtain white matter parcellation of the individual Brodmann area volumes? >>> >>> Thanks, >>> >>> Vinny >>> >>> _______________________________________________ >>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >>> be* >>> https://secure-web.cisco.com/1-c_XiUItD_cErDHtESMG8WcdYK4wx-hALr6IiQH_WL2b2DbP2ZR5zX1WwQzZwc1EdZ5JErtFa8c09_yB14vQrVUeAgSa-mrALaU0hf5qwgw0RWrKhYvny8d6Cby2QXzX-399VWOZ1fppD6lk_Atdgo8jRE0Y0NhVAhH3ClVxMaTR4FBeup_kaU8MojSypOXCfedWrgUmeVe12GtL3LoUJenLy79IrZsFUJseXNaTVZUIiqa4pZ41p-Tf1Yr4Ynayqp6YZxDKCp6bOeM48XlFZw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> <https://secure-web.cisco.com/1XPT6Fbpm6OPt_GvWVIsGXkx3tVw-af5z2c71ybRrUDrCELV2HU14Z0pZ4zkV81_g4WPn9CmLnCrzZ9R-ws2rCm9isgUA8nxrejdZWGn2XKDXv6k5WG46ksPYWzPDnwboVj3L3_NwMkfBiBQjwNq_UbqHi2PpeqsEiiEIhA3_G_WL6FScjnmcAHmxI_QcS55a7qrxQ0LDkA4E9vVb3Jku8awsyK9L5ZVLgwa9jNBU5VzRLZ0in3ks9uRaZOv22iSaZaaIP6LExb-CfWeowwYKMg/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://secure-web.cisco.com/1-c_XiUItD_cErDHtESMG8WcdYK4wx-hALr6IiQH_WL2b2DbP2ZR5zX1WwQzZwc1EdZ5JErtFa8c09_yB14vQrVUeAgSa-mrALaU0hf5qwgw0RWrKhYvny8d6Cby2QXzX-399VWOZ1fppD6lk_Atdgo8jRE0Y0NhVAhH3ClVxMaTR4FBeup_kaU8MojSypOXCfedWrgUmeVe12GtL3LoUJenLy79IrZsFUJseXNaTVZUIiqa4pZ41p-Tf1Yr4Ynayqp6YZxDKCp6bOeM48XlFZw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <https://secure-web.cisco.com/1XPT6Fbpm6OPt_GvWVIsGXkx3tVw-af5z2c71ybRrUDrCELV2HU14Z0pZ4zkV81_g4WPn9CmLnCrzZ9R-ws2rCm9isgUA8nxrejdZWGn2XKDXv6k5WG46ksPYWzPDnwboVj3L3_NwMkfBiBQjwNq_UbqHi2PpeqsEiiEIhA3_G_WL6FScjnmcAHmxI_QcS55a7qrxQ0LDkA4E9vVb3Jku8awsyK9L5ZVLgwa9jNBU5VzRLZ0in3ks9uRaZOv22iSaZaaIP6LExb-CfWeowwYKMg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> _______________________________________________ >> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/1-c_XiUItD_cErDHtESMG8WcdYK4wx-hALr6IiQH_WL2b2DbP2ZR5zX1WwQzZwc1EdZ5JErtFa8c09_yB14vQrVUeAgSa-mrALaU0hf5qwgw0RWrKhYvny8d6Cby2QXzX-399VWOZ1fppD6lk_Atdgo8jRE0Y0NhVAhH3ClVxMaTR4FBeup_kaU8MojSypOXCfedWrgUmeVe12GtL3LoUJenLy79IrZsFUJseXNaTVZUIiqa4pZ41p-Tf1Yr4Ynayqp6YZxDKCp6bOeM48XlFZw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1ZVwlNh8w2dkw0lUVsXw6gRvsfWpZi32SKA877TnjfxqHD2Ek-e6DRju8lQly6Rv6Ur3MuLYSsDHwTnPqWXgyG-4wzDbBdRjEQTdmaGqlxLcJaAOUzHUJz6ag21jyMhMaic3CBLNn__1AlQ_R62Py-F48ce9z4ceYtyHTqeTap1sY228lZZIHa1Fm4XpTgGFF1q3UaMe7KQYoJBdQqq8ImfxGGcjHnjGSgri8WS9baOjQZGkyVXoSuOHs5nz0S-nikTJqhyda4EL9GF09wQQmHw/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://secure-web.cisco.com/1-c_XiUItD_cErDHtESMG8WcdYK4wx-hALr6IiQH_WL2b2DbP2ZR5zX1WwQzZwc1EdZ5JErtFa8c09_yB14vQrVUeAgSa-mrALaU0hf5qwgw0RWrKhYvny8d6Cby2QXzX-399VWOZ1fppD6lk_Atdgo8jRE0Y0NhVAhH3ClVxMaTR4FBeup_kaU8MojSypOXCfedWrgUmeVe12GtL3LoUJenLy79IrZsFUJseXNaTVZUIiqa4pZ41p-Tf1Yr4Ynayqp6YZxDKCp6bOeM48XlFZw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1vKsyHZAPqbjZluPk8SL_Ri2zcUkIaDvzZGoDNvm-qvzotffi99M6--b1D0z6yTLaXYh97oNL1AaCWnz_avAmfSWbHVEGz3RIGS5ztHtEZVOQThw2XFozXHd22GfG0Hfdb0wMppyAf8kNt-cqNScbtftoRlj1vM4MFZz1hF1ss6MjKDiCK2HnLz_2i8XMwHHbKyCfEpYzjf5NnScoAuQSA-txpO07pzMpjtEUDpDsjklEPtVCbS8oHT44ctZPGxAM2X_guWzqYlz0RS5CxL3sIw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@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/1-c_XiUItD_cErDHtESMG8WcdYK4wx-hALr6IiQH_WL2b2DbP2ZR5zX1WwQzZwc1EdZ5JErtFa8c09_yB14vQrVUeAgSa-mrALaU0hf5qwgw0RWrKhYvny8d6Cby2QXzX-399VWOZ1fppD6lk_Atdgo8jRE0Y0NhVAhH3ClVxMaTR4FBeup_kaU8MojSypOXCfedWrgUmeVe12GtL3LoUJenLy79IrZsFUJseXNaTVZUIiqa4pZ41p-Tf1Yr4Ynayqp6YZxDKCp6bOeM48XlFZw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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