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 thal

[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 Freesurfer@nmr.mgh.harva

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: E

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 FreeSurfe

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] 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 corte

[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

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 mer

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 correct

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 t

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 4:3

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 and