[Freesurfer] Beta Extraction

When I ran the following command (with our data), I got the average beta values for each segmentation i.e. only 5 beta values (as opposed to 5 beta values for each subject). mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf beta.clusters.dat That said, is it necessarily to run the

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Hi Doug, Sorry to bother, maybe my last message got lost. Do you think you can advice me on this type of registration? Thanks! Best Francesca On Fri, Feb 22, 2019, 11:44 PM Francesca Strappini < francescastrapp...@gmail.com> wrote: > What is the bes

Re: [Freesurfer] Beta extraction

When I ran the following command (with our data), I got the average beta values for each segmentation i.e. only 5 beta values (as opposed to 5 beta values for each subject). mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf beta.clusters.dat That said, is it necessarily to run the

Re: [Freesurfer] mri_vol2surf for sampling spmT_0001.nii on pial surface

Hi Michael you can use either --projfrac-avg or --projdist-avg (dist I guess if you want to specify 10mm). Note that this is an average along 1D (the surface normal direction), not in a volume window cheers Bruce On Wed, 27 Feb 2019, Michael Jordan wrote: External Email - Use Ca

[Freesurfer] MD with dt_recon

External Email - Use Caution Sorry, I just found in a previous post by doug that ADC is the same as MD? *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 __

[Freesurfer] MD with dt_recon?

External Email - Use Caution Hello, There is no mean diffusivity output with dt_recon. How would you suggest to create MD images? Could you simply divide the adc.nii.gz map by 3? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab

[Freesurfer] mask-FA mri_vol2vol issue - followup

External Email - Use Caution Hello, I am still having the same issue as in my previous post. I have successfully run dt_recon and upon looking at the images there seems to be no issue with the registrations of outputs including the FA, lowb and other images. I wanted to mask my F

Re: [Freesurfer] mri_vol2surf for sampling spmT_0001.nii on pial surface

External Email - Use Caution Hi Bruce, thank you it worked! Another short question: I want mri_surf2vol to assign the average of all volume voxel values within 10 mm to the corresponding vertices. So if there is only one voxel value greater than zero in the volume, all vertices

Re: [Freesurfer] Question about Label

the cortex.label is built based on a bunch of rules (e.g. surface locations next to the CC are not cortex), and so varies across subject depending on structure size and geometry cheers Bruce On Wed, 27 Feb 2019, 310913949 wrote: External Email - Use Caution Hi Freesurfer P

[Freesurfer] Question about Label

External Email - Use Caution Hi Freesurfer Pros?? I want to know how the label file is generated?Is it the *h.cortex.label generated after mapping the vertices into the space of the fsaverage? If yes, why different subjects dont have the same vertices number of the lh.corte