[Freesurfer] Passcode Request

External Email - Use Caution Hello, I am trying to extract files in the 7zip download for the VurtualBox VM and it requires a passcode. Could you please send me the passcode required for this step. Thanks, Ryan ___ Freesurfer mailing

[Freesurfer] Large number of false negative MS lesions in SAMSEG

External Email - Use Caution Hello, I am testing SAMSEG on my group of MS patients. Unfortunately, even when dropping threshold to 0.005 I have large number of false negative lesions left behind by SAMSEG (80% in about 75 cases I tried), which are clearly visible lesions. I ran/ch

Re: [Freesurfer] running mri_glmfit with atlas

Yes, look at the ROI analysis tutorial (eg, asegstats2table or aparcstats2table then mri_glmfit with the --table option) On 8/13/2022 2:22 AM, Hye Min Shin wrote: External Email - Use Caution Hello experts, While going through GroupAnalysis tutorial for freesurfer (*MailScanner has

Re: [Freesurfer] FSFAST first level covariates

Those look like they are the same coding scheme. What is different? You can only have one offset. The Self vs Valence -a 2 -a 4 is not testing for an interaction. If you want an interaction you have to create a new variable which is SelfRating*ValenceRating. On 8/10/2022 2:38 PM, Angela Fang

[Freesurfer] Large number of false negative MS lesions in SAMSEG

Hi Martin, Can you try to remove the lesion intensity constraint on the T2 data (i.e., by modifying your command with --lesion-mask-pattern 0 1 0) for a couple of cases and let us know if it helps? If not, would you be able to share with us one case where it fails? FYI: you can save a lesion

Re: [Freesurfer] FSFAST first level covariates

External Email - Use Caution The two coding schemes are different because the second one does include the self*valence variable you’re talking about, whereas the first one doesn’t. I only included the 2nd offset because you suggested to someone else to include it (see https://s

[Freesurfer] transform amygdala mask from FS to native space

External Email - Use Caution Hi Freesurfer Developers, I have segmented hippocampal/amygdala masks for my participants with the segmentHA_T1.sh script, but I am wanting to transform these masks into native space for analysis. I have tried using mri_convert (command below), howev

Re: [Freesurfer] Parcellation issue

External Email - Use Caution Hi Reuben, What template are you trying to use? Regards, Thomas On Tue, Aug 9, 2022 at 8:39 PM Addison, Reuben wrote: > > > I want to use a different template apart from the MNI for my parcellation > (Yeo_JNeurophysiol11_FreeSurfer.zip). Below are

Re: [Freesurfer] Parcellation issue

The Yeo et al, 2011 template Reuben A. Get Outlook for iOS From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Thomas Yeo Sent: Sunday, August 14, 2022 6:59:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] Parcellation

Re: [Freesurfer] Parcellation issue

External Email - Use Caution Hi Rueben, I am afraid I don't understand your question. The Yeo networks are available in fsaverage and FSL MNI152 space. If your data is already in fsaverage or FSL MNI152 space, you can simply use the networks directly without running recon-all. C