Re: [Freesurfer] mris_register error

Hi Greg, try using recon-all -make all then rerun the V1 stuff. cheers Bruce On Tue, 9 Mar 2010, Gregory Dierksen wrote: > > Hello, > > So I'm attempting to use the V1_predict script to generate a primary > visual cortex label and had been receiving an error message. I was able > to track down

[Freesurfer] mris_register error

Hello, So I'm attempting to use the V1_predict script to generate a primary visual cortex label and had been receiving an error message. I was able to track down the error to the mris_register command: mris_register -inflated -a 4096 -dist 10.0 -parea 1.0 \ /surf/lh.sphere \ /label/lh

Re: [Freesurfer] wm edits and control points

Hi Dana, you can do autorecon2-cp and it will do both things (the wm comes after it in the stream anyway) cheers Bruce On Tue, 9 Mar 2010, Dana W. Moore wrote: > Hello everyone, > > There is an image that needs white matter edits (editing voxels) as > well as control points. I know the two com

[Freesurfer] wm edits and control points

Hello everyone, There is an image that needs white matter edits (editing voxels) as well as control points. I know the two commands I need to re-run are autorecon2-cp and autorecon2-wm. Can I do both kinds of edits and somehow combine the -cp and -wm commands, or do I need to do the control

Re: [Freesurfer] mris_volsmooth without registration

Just give it a reg with the identity matrix. doug Chris Filo Gorgolewski wrote: > Hi, > my functional runs are already coregistered and resliced to > mri/orig.mgz (I use ROI from aseg+aparc and I want to avoid > downsampling) so in theory I do not need to use bbregister to prepare > registration

[Freesurfer] mris_volsmooth without registration

Hi, my functional runs are already coregistered and resliced to mri/orig.mgz (I use ROI from aseg+aparc and I want to avoid downsampling) so in theory I do not need to use bbregister to prepare registration file for mris_volsmooth. However, --reg argument in mris_volsmooth is mandatory. So far I wa

Re: [Freesurfer] bbregister

Hi, I used the commands below, having specified the file paths. bbregister --s ${subject} --mov ${pet_nii} --bold --init-fsl --reg ${register_dat} mri_vol2surf --mov ${pet_nii} --reg ${register_dat} --hemi lh --projfrac 0.5 --o ${subj_dir}/bl/lh.pet.mgh mri_vol2surf --mov ${pet_nii} --reg ${regi

Re: [Freesurfer] bbregister

Hi Corinna, What is the command line that you are trying. On Tue, 9 Mar 2010, corinna bauer wrote: > Hello, > I am running bbregister with pet scans and a number of the subject's > registrations were poor. What is the best way to fix inaccurate > coregistrations from bbregister? > > Regards,

Re: [Freesurfer] Cortical thickness measurement

you can look at our recent Cerebral Cortex paper and see what BAs we estimate On Tue, 9 Mar 2010, Janani Dhinakaran wrote: > Looking to isolate and measure the thickness of certain brain cortex areas > eg- broca's or sensory cortex > On 8 March 2010 19:58, Allison Stevens wrote: > >> which labe

Re: [Freesurfer] Cortical thickness measurement

Looking to isolate and measure the thickness of certain brain cortex areas eg- broca's or sensory cortex On 8 March 2010 19:58, Allison Stevens wrote: > which labels are you looking for information on? > > -- > > On Mon, 8 Mar 2010, Janani Dhinakaran wrote: > > That command gives several options

[Freesurfer] bbregister

Hello, I am running bbregister with pet scans and a number of the subject's registrations were poor. What is the best way to fix inaccurate coregistrations from bbregister? Regards, Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] How to verify cerebellum segmentation

Hi Bruce and Sita, Do you have any suggestions after seeing the modified and original data? Thanks a lot, Gergo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information