Re: [Freesurfer] Hippocampal-Amygdala subfields error

External Email - Use Caution Hi Eugenio, Did you have chance to review the error that I have reported some days ago when I ran the hippocampal and amygdala command? It was happened only in 17 subjects (sample size 295). I rerun the HippocampalSubfieldsandAmygdalaNuclei command

Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

Hi Davide, a centos7 distribution will use the same libraries as a centos6 distribution. What kind of issues are people reporting? Are there command line errors associated with these issues? Andrew From: on behalf of "Vanzo, Davide" Reply-To: FS Help Date: Tuesday, September 25, 2018 at

Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

External Email - Use Caution Andrew, Unfortunately our users have reported issues using freeview.bin in CentOS 7. The reason being that the CentOS 6 binaries that you provide depend on an ancient version of VTK. Since you provide nightly build for CentOS 7, would it be possible

Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution Hi Freesurfer Experts, About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline. I tried to

Re: [Freesurfer] longitudinal hippocampal aseg editing

Hi Rebecca, I see. Generally, it should behave in the same way as cross sectional processing: If both aseg.mgz and aseg.auto.mgz exist, and they are different, then  the file aseg.manedit.mgz is created from the differences (and if an  aseg.manedit.mgz file also exists, then its contents are

[Freesurfer] Research Assistant Job, Chicago, IL

External Email - Use Caution Research Assistant job available at Northwestern University’s Mesulam Cognitive Neurology and Alzheimer’s Disease Center in Chicago, IL. Job Summary: This position is within Dr. Emily Rogalski’s laboratory, which focuses on aging and dementia

Re: [Freesurfer] Vertex position

Hi Karin yes, but can you explain what you mean by "where"? (x,y,z) Talairach location? Lobe? Parcel? cheers Bruce On Tue, 25 Sep 2018, Karin Westin wrote: External Email - Use Caution Hi! Is it possible to retrieve a map or table indicating exactly where on the

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

External Email - Use Caution I posted a reply with the dwi_orig.nii screenshots on Friday, but they did not show up on the list. Yes, the dwi_orig.nii images appear the same as the dwi.nii.gz images. Also, I ran them through TrackVis/DTK and they came out correct, so it seems to

Re: [Freesurfer] error with trac-all -prep

External Email - Use Caution Hi Anastasia, Thanks for your reply and your recommendation to use mri_binarize to set up ROIs. Actually, I was able to use the new thalamic tool Eugenio had set up with good segmentation. It's just that I had noticed thalamic labels in the

Re: [Freesurfer] error with trac-all -prep

Hi Vinny - Glad that things worked out. I'll defer to Eugenio about the thalamic parcellation, but in general mri_binarize --match allows you to create an ROI from all the voxels in a segmentation map that have a specific segmentation ID. a.y On Sep 25, 2018 7:33 AM, Vinny K wrote:

[Freesurfer] Vertex position

External Email - Use Caution Hi! Is it possible to retrieve a map or table indicating exactly where on the cortex a vertex with a specific id number is located? Best and thanks, Karin ___ Freesurfer mailing list

Re: [Freesurfer] error with trac-all -prep

External Email - Use Caution Hello Anastasia, The approach worked great and I was able to get the required TRACULA outputs from each step. According to the FreeSurfer Lookup Table, there are thalamic parcellation labels from 8001 - 8014. How can I access and visualize these