Re: [Freesurfer] Group analysis

On 3/9/20 5:53 PM, Hengameh Marzbani wrote: > > External Email - Use Caution > > Hello Freesurfer developers, > 1- I want to extract the uncorrected clusters from the uncorrected > significance maps obtained from mri_glmfit for structural data (to illustrate > cluster, size, location,

[Freesurfer] Group analysis

External Email - Use Caution Hello Freesurfer developers, 1- I want to extract the uncorrected clusters from the uncorrected significance maps obtained from mri_glmfit for structural data (to illustrate cluster, size, location, and significance) like abs.sig.cluster.summary

Re: [Freesurfer] freeview failed to load Surface overlay

Hi Meike, Would it be possible to send us one of the sig.mgh files to inspect? Thanks, Ruopeng On 3/9/20 3:24 PM, Meike Hettwer wrote: External Email - Use Caution Dear freesurfer experts, I am currently running a very basic correlation with two groups (gender, which I am not

[Freesurfer] freeview failed to load Surface overlay

External Email - Use Caution Dear freesurfer experts, I am currently running a very basic correlation with two groups (gender, which I am not interested in), age and genetic scores (the latter of which I am interested in) included in the glm. Atm I am using a DODS model (0 0 0

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution Dear Tim, The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will affect the process Recon-all? If yes, how would it impact my output results? Regards Frank From:

Re: [Freesurfer] Converting ANTs nonlinear transform to .m3z

Have you tried using mri_warp_convert? You can convert from ITK format (ANTs) to M3Z via: mri_warp_convert --initk antswarp.nii.gz --outm3z fswarp.m3z --insrcgeom src.nii.gz This way you can also specify the missing source geometry information required for the m3z. Andrew

[Freesurfer] Tracula Inquiry

External Email - Use Caution Hi, I am seeing the following error: Admins-iMac:XXXneurology$ trac-all -prep -c XXX.24.14Configfile.rtf Missing }. Missing }. }: Command not found. Missing }. red255green255blue255: Command not found. }: Command not found. Missing }. }: Command

[Freesurfer] Query regarding FA quantification in ROI

External Email - Use Caution Dear Freesurfer team, I have done FA quantification in brainstem substructures using two ways and got slightly different results. First, I used dMRI Data Analysis Processing Stream with the following steps (after brainstem segmentation followed by