Re: [Freesurfer] mri_cor2label --surf "dim mismatch between surface"
Not sure what you are trying to do. extracting the vent vol to a surface does not make sense to me On 1/28/2022 1:23 PM, Zeng, Qi wrote: External Email - Use Caution Hi, I saw the same question has been asked and no answer was provided: I run "mri_cor2label --c fsaverage/mri/aseg.mgz --id 4 --l fsaverage/label/Left-Lateral-Ventricle.label --surf fsaverage lh" - to hopefully extract lateral ventricles volume into a overlay of surface base. however, gave me error: "dim mismatch between surface (100515) and input (16777216)". What should I change? BTW, Also have questions for the following steps and hope you can answer that too: 1. convert surface-based label to volume, "mri_label2vol --label fsaverage/label/Left-Lateral-Ventricle.label --subject fsaverage --hemi lh --identify --temp fsaverage/mri/T1.mgz --o fsaverage/mri/lh.Left-Lateral-Ventricle.nii --proj frac 0 1 0.01 2. Better ROI with mri_binarize "mri_binarize" --dilate 1 -erode 1 --i fsaverage/mri/h.Left-Lateral-Ventricle.nii --o fsaverage/mri/h.Left-Lateral-Ventricle.nii --min 1 3. constrain the thick ROI "mris_calc -o fsaverage/mri/h.Left-Lateral-Ventricle.nii fsaverage/mri/h.Left-Lateral-Ventricle.nii mul fsaverage/mri/h.Left-Lateral-Ventricle.ribbon.mgz 4. Questions: Are the aforementioned steps correct? In the end, if I have a couple of ROIs, what should I use to combine them. or just load them separately with lh.white and lh.pial. Best, Qi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Transform a surface (e.g., lh.white) with a register.dat (12 dof)
See the --lta option to mris_apply_reg On 1/28/2022 10:07 PM, Yixin Ma wrote: External Email - Use Caution Hi FreeSurfer developer, I want to transform surfaces files (lh.white, lh.pial, rh.white, and rh.pial) with a registration matrix that has 12 degrees of freedom. Is there a function in FreeSurfer that can do so? Very best, Yixin Ma ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Transform a surface (e.g., lh.white) with a register.dat (12 dof)
External Email - Use Caution Hi FreeSurfer developer, I want to transform surfaces files (lh.white, lh.pial, rh.white, and rh.pial) with a registration matrix that has 12 degrees of freedom. Is there a function in FreeSurfer that can do so? Very best, Yixin Ma ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Reading files from a hard drive (on Windows in the Fressurfer Ubuntu VM)
External Email - Use Caution Please see the updated documentation in the previous announcement about how to share/mount an external hard drive at https://secure-web.cisco.com/1yjgxLva8l6O68IkaN5KFrOHCn5Y3OV8mnxI6DMsZ2kYAvvxvG8_uNd14rVsOQvpDwi8RbbWBbmnucNpH_uJryUAyXyN3Bkwf9NIlKXsw6xoF71rrSDWnbiBZbErF4cTv9Be9CHkJZIA-vj93zx5YXUYVEQ07qta6KUNesLdCJWqIVSrIX8NBq4NHw0GwvvkEljR2PDQ6MdAKF72Z7B5bQdKBybZg28lR9RRrwPNaEOI-gjPgO--B4y_URZsKPzcyZTFS3L_D4IMYsRocMR3cD_k78OLEyl5jhe1PoK5TnNWvBatcv-ELZk-c9KZo3wXQ9AljngQF8b3XdS3VFPO7yQ/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FVM_67 - R. krystaly (kryst...@hku.hk)January 27, 2022 at 19:33 External Email - Use Caution I’m not sure if this is the correct way (please see the attached) to solve my problem. Please kindly advise. Thank you for your attention. Best regards, Krystal From: fsbuild Sent: Tuesday, January 25, 2022 9:57 AM To: freesurfer@nmr.mgh.harvard.edu Cc: ts...@rcmd.org Subject: Re: [Freesurfer] Reading files from a hard drive (on Windows in the Fressurfer Ubuntu VM) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1oDBI5mZnFPqTOWdVRbiAc7B-sr876yiNnvgoHpRWeSrCRpbZVm2fdlhVkRvj1XRRNGPvD3pajurjMNa2YxgbmNP50xEJpIZuRdxt8flfQX-gCZ-rRUIJNEUFr4TzamTiizbgmlCtk2M0D-131ALPChNxFqnPHAnHuA9frzg9rFYHFUH0QObLnSwsj1-ZanS8d2WaYxuflYwrHvoT-ORoOEAEpaSIGJnxBxrw1bIfZ24LeJl0iXPd2B5WHsS7ImjyQ7tbch8v-A4r0IknEixXp-1vLa5U2uV0y5U5oaiXRWksbkaaS_eaNri-yr5-H44HMsVLau1I8JT7Qj_SINNG-A/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
[Freesurfer] Freesurfer Ubuntu VM documentation updated
External Email - Use Caution The Freesurfer Ubuntu VM documentation has been updated to describe how to mount an external drive plugged into the Windows machine in the VM. See towards the bottom of the page under "Share a directory ...", https://secure-web.cisco.com/12kQxE07BvTEpf6PBZdobfuBYlzrxz4JsMUZ649qdrKnj4l1ZBkeje5cqejHxIsbL4WhOEa2SlN5v0znEPkZm8FP7WEtBW8tUJ5FVGRzU8tqO9UbWIvjGdajV2JUmK37uhC1lkM8lBc0zyE9w4GzTGDYbxuTUyVvS4qG6X3wKokxkUmDQ-yErx9jTjqySApsEn0PQDr-hy6jymsbBNptCb7pUOr0YkF4tUt3UPV6C45wtgyIBMtFz2A4zaMUdNfeKGo6UNa3rDJ_oM1Hgw6MPL4wGOA-TqdjXiuy7JAMygPsY4LTo1Q69UOznhjD0KJGpdgq4m2RgowrWlj9bki8zMQ/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FVM_67 - R. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_cor2label --surf "dim mismatch between surface"
External Email - Use Caution Hi, I saw the same question has been asked and no answer was provided: I run "mri_cor2label --c fsaverage/mri/aseg.mgz --id 4 --l fsaverage/label/Left-Lateral-Ventricle.label --surf fsaverage lh"- to hopefully extract lateral ventricles volume into a overlay of surface base. however, gave me error: "dim mismatch between surface (100515) and input (16777216)". What should I change? BTW, Also have questions for the following steps and hope you can answer that too: 1. convert surface-based label to volume, "mri_label2vol --label fsaverage/label/Left-Lateral-Ventricle.label --subject fsaverage --hemi lh --identify --temp fsaverage/mri/T1.mgz --o fsaverage/mri/lh.Left-Lateral-Ventricle.nii --proj frac 0 1 0.01 2. Better ROI with mri_binarize "mri_binarize" --dilate 1 -erode 1 --i fsaverage/mri/h.Left-Lateral-Ventricle.nii --o fsaverage/mri/h.Left-Lateral-Ventricle.nii --min 1 3. constrain the thick ROI "mris_calc -o fsaverage/mri/h.Left-Lateral-Ventricle.nii fsaverage/mri/h.Left-Lateral-Ventricle.nii mul fsaverage/mri/h.Left-Lateral-Ventricle.ribbon.mgz 4. Questions: Are the aforementioned steps correct? In the end, if I have a couple of ROIs, what should I use to combine them. or just load them separately with lh.white and lh.pial. Best, Qi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
