External Email - Use Caution That worked, thank you so much!
Regards, Fahad ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <yhuan...@mgh.harvard.edu> Sent: Wednesday, July 5, 2023 9:53 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_segstats dimension mistach You don't often get email from yhuan...@mgh.harvard.edu. Learn why this is important<https://secure-web.cisco.com/1Dk3IomBhiwa4sFDW-VA4Si0nOb2_WAJpbxqivfkQn46Ey78V3m_6r_UfoHxXKVWiUIh-COSaW6-TT5Q6-lZhcA-NrlhGVgdTUEcNz4P9ShOJP9iNuA5lrB5ZEJ2bFCbHPknDZ7jqfN4uwRFuuEmFzY-D5QB2E20Lv4axecXFYkek2nNkL-lC_ul37ZdnU0HDIidVNN5Yv4G3LHRLUtzgx1lTfo_UQ3bzBn2eRwbfbE1q9ZsDeDQrd2avd99J1mh2artubXlbd8v-UmGv0Fb9SO5DWdI4w4hhwB00OAEoDz8Ju8IW6yDknh_twbba0FUGOWS0r-Ejkm-9wbqOWaHDmA/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification> External Email - Use Caution Hi Fahad, Here is the wiki page about how to Convert from FreeSurfer Space Back to Native Anatomical Space - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ra2U8cDomVFQCO-1Aat6B6-AjtuLqzp5FeIV0ef8j4TJy4jL5YVqk0ZY85q9VvQDjTt7JlbClqTkflt4zTQ4sqfTYqGRXuNdiCGhMnf5d67sEtbQk0YI6f7UvWZJu6UCuW1IXSUYcBDEVhL02QNX1vzQWPXde2i0UAneFHWY0vBcouq8FIVZYxqvbEkbJ4v30ojDYiYpTnmFfhGcpCpr7FzDbbLGEvclrtC-LSQ3WE35x99pDRZl4BNiJhyRkKJyvLE7Wsd2eoH8yY92UteJy2ABFzFlR6vfHOchiwVZOvnDT-bb4MeVCw0cHGsGqKvRnMD4wKABsFD843JK2iLEOA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat<https://secure-web.cisco.com/1SH-F86njclC8pQKcB6nkwsqK8lnEDnPON_A24-6CmCwRHC_v0s6AwvY_foOYGXPrbz_PgXgmdPkQnHYy_AMudJENZoBcBNcrqdJGYd-N6ZKQjjSH-gzCI5Dq5ZHU2wFNKxRh944qf6UZNgqhb4s_XDC669KdGDt4GGk_mpnPRMKrIRyGvLfJb8vKw02AHSq1SM528T730feGzUsjm9FM5CgiF3QW5mg-UlGeOlPUDGd9xvS0cKt60Wny7zkFNwJMyH553-KKUKzzeyOvA09Wnw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat> Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Fahad Hannan Sent: Monday, July 3, 2023 3:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_segstats dimension mistach External Email - Use Caution Hello, I'm trying to run the mri_segstats on different input volume. The input volume has the same dimensions as the original volume used to perform recon-all. However, when trying to use the following command: "mri_segstats --seg $SUBJECTS_DIR/P6V1/mri/wmparc.mgz --sum $SUBJECTS_DIR/P6V1/stats/T2lobestest.stats --id 3201 4201 3203 4203 3204 4204 3205 4205 3206 4206 3207 4207 --in T2_Map.nii.gz --in-intensity-name norm --in-intensity-units MR --etiv --subject P6V1 --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt" I get a dimension mismatch error: ERROR: dimension mismatch between input volume and seg input 112 112 80 seg 256 256 256 Seems like during the recon-all process, freesurfer changed the dimensions of the segmentation file to 256 256 256. Is there a way I can resample the segmentation file to the input files dimensions, I know I can resample the input to the norm.mgz file but I do not want to tamper with the input file. Thanks, Fahad
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
