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
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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dgreve@mgh.harvard.edu wrote:
which version of FS are you using?
On 2/5/2021 10:02 PM, Vinny K wrote:
External Email - Use CautionHello,
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 listFreesurfer@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/1XPT6Fbpm6OPt_GvWVIsGXkx3tVw-af5z2c71ybRrUDrCEL...
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 <dgreve@mgh.harvard.edu mailto:dgreve@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 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/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 <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/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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dgreve@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 CautionI am using freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
On Tue, Feb 9, 2021 at 9:55 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
which version of FS are you using?
On 2/5/2021 10:02 PM, Vinny K wrote:
External Email - Use CautionHello,
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 listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ZVwlNh8w2dkw0lUVsXw6gRvsfWpZi32SKA877TnjfxqHD2... 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/1ZVwlNh8w2dkw0lUVsXw6gRvsfWpZi32SKA877TnjfxqHD2... 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 listFreesurfer@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/1ZVwlNh8w2dkw0lUVsXw6gRvsfWpZi32SKA877TnjfxqHD2...
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 <dgreve@mgh.harvard.edu mailto:dgreve@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 <dgreve@mgh.harvard.edu <mailto:dgreve@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 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/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 <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/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 <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/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 <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/1vKsyHZAPqbjZluPk8SL_Ri2zcUkIaDvzZGoDNvm-qvzotffi99M6--b1D0z6yTLaXYh97oNL1AaCWnz_avAmfSWbHVEGz3RIGS5ztHtEZVOQThw2XFozXHd22GfG0Hfdb0wMppyAf8kNt-cqNScbtftoRlj1vM4MFZz1hF1ss6MjKDiCK2HnLz_2i8XMwHHbKyCfEpYzjf5NnScoAuQSA-txpO07pzMpjtEUDpDsjklEPtVCbS8oHT44ctZPGxAM2X_guWzqYlz0RS5CxL3sIw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you very much!
On Wed., Feb. 10, 2021, 10:05 a.m. Douglas N. Greve, dgreve@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 CautionThanks 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 dgreve@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 CautionI am using freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
On Tue, Feb 9, 2021 at 9:55 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
which version of FS are you using?
On 2/5/2021 10:02 PM, Vinny K wrote:
External Email - Use CautionHello,
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 listFreesurfer@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_WL2b2D... 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_WL2b2D... 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 listFreesurfer@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_WL2b2D... 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_WL2b2D... 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 listFreesurfer@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_WL2b2D...
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Vinny K