Re: [Freesurfer] Time course thalamic subregions

External Email - Use Caution Hi, I have used: mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f-in-anat.mgh mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 --max 8114 --o merged_ROIs.nii.gz mri_segstats --seg merged_ROIs.nii.gz --id 1 --i f-in-anat

Re: [Freesurfer] what is the right manual correction when ?h.white extends into gray matter

External Email - Use Caution Hello Bruce, thank you very much for your response. I just uploaded a file. It is called 109_Caroline_Chwiesko_8-23-2019.tar.gz. And I uploaded a file with some example coordinates. Thank you very much for taking the time and looking at it! Best Caro

Re: [Freesurfer] extra cerebral CSF

You can use samseg in the development version. Keep in mind that it is somewhat unstable. Make sure to give it an mgz and not a nifti or mgh file On 8/23/2019 2:51 PM, Jared Nielsen wrote: External Email - Use Caution I've seen some previous posts about a measure of extra cerebral CSF

[Freesurfer] extra cerebral CSF

External Email - Use Caution I've seen some previous posts about a measure of extra cerebral CSF coming in the future. Is the measure now available, or is it still in the works? If it's still in the works, can an ETA be provided? Thanks, Jared __

Re: [Freesurfer] TRACULA - OrientLAS issue for a subject

Hi Daniel - You can confirm if the orientation is different from your other scans by running mri_info directly on the dicom. If these two subjects were scanned in a completely different orientation than the rest of the subjects in your study, e.g. coronal vs. axial, if does raise the question of

Re: [Freesurfer] freeview crash -- petsc error when opening volume

External Email - Use Caution Good morning Ruopeng, thank you for your continued assistance! Unfortunately, I get the same error using the CentOS6 dev version. I tried the CentOS7 dev version, however this led to a series of library errors, the majority of which are unsolvable on

Re: [Freesurfer] recon_all hires

Hi Mona if you upload your gzipped and tarred subject dir we will take a look (or if it is somewhere accessible just point us to the network location and give us access) cheers Bruce On Fri, 23 Aug 2019, falk.luesebr...@med.ovgu.de wrote: External Email - Use Caution Hi

Re: [Freesurfer] Help with using family as random effect in sibling study

Hi Doug, thanks for getting back to me! So since we have just one pair of siblings per family, this way will not work? -- Casey Hopkinson Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, M

Re: [Freesurfer] Help with using family as random effect in sibling study

You could create a class for each family and assign each pair to a class. But this will not work unless you have multiple pairs per family for each family. On 8/23/2019 9:01 AM, Hopkinson, Casey E wrote: Hi everyone, Just wanted to follow up with this in case anyone may have an idea of if this

Re: [Freesurfer] Converting surface coordinates to MNI coordinates

Yes, this is confusing. We can apply a transform to the MNI305 coords to get approx Tal coords. If QDEC is showing you "Tal" coords, then this is what has happened. I don't know what other papers reported. If they used the command line stream (ie, no QDEC), then it is probably MNI305 On 8/22/20

Re: [Freesurfer] Gender and age based reconstruction

Yes, it does everything without regard to age or gender. The full processing stream is pretty complicated, but it does segment various structures (white matter and various GM structures) On 8/22/2019 4:02 PM, Carissa Liana Grijalva wrote: External Email - Use Caution Hello FreeSurfer S

Re: [Freesurfer] Help with using family as random effect in sibling study

Hi everyone, Just wanted to follow up with this in case anyone may have an idea of if this can be done. Thanks! -- Casey Hopkinson Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 021