[Freesurfer] over-estimated brain volume based on (recon-all / recon-all-clinical) ?

External Email - Use Caution Dear FS developers, Hi, I am very happy that we can use new features of FreeSurfer (e.g., recon-all-clinical.sh, SynthSeg, SynthSR, etc.) While using a variety of functions from FreeSurfer (v7.3.2 and v7.4.1), we would like to hear the answers to the

[Freesurfer] WM Hypointensities

External Email - Use Caution Hi Freesurfer experts! I am hoping to extract the wm-hypointensity data from some recon-all-clinical runs. I was able to extract aseg.stats information correctly but noticed there was no information regarding the wm-hypointensities. Is this

Re: [Freesurfer] Tracula statistics outputs for version 7.2

External Email - Use Caution Hi King-Wai: I have been running Tracula on 7T images and it keeps giving me an error. The error is as follows: copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_2 Unmatched '"'. I have attached my config file. Can you please let me know

Re: [Freesurfer] Tracula statistics outputs for version 7.2

External Email - Use Caution Hi Chiara - Please ignore the previous email. I set my doB0 = 0, but it gives me this error message: copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_4 ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for

Re: [Freesurfer] Tracula statistics outputs for version 7.2

External Email - Use Caution Hi Alan, It looks like you have specified the ncpts variable but not the pathlist. If you do not specify pathlist, TRACULA will include all 42 tracts by default, so your pathlist and ncpts variables will have different lengths. If you want to

Re: [Freesurfer] Tracula statistics outputs for version 7.2

External Email - Use Caution Hi King-Wai/ Chiara Thank you for your excellent suggestions. Chiara: I have made the changes you suggested. Can you please check if the config file looks workable? King-Wai - I made the change you suggested. But the problem still persists. I have

[Freesurfer] freesurfer overlay function

External Email - Use Caution can we use freeview for comparing 2 MRI in a overlaying 3D model in one windows ? best regards ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] pass code for FS_7_2_0_ubuntu_18_04_06.ova

External Email - Use Caution Hi, Could I please get the pass code for FS_7_2_0_ubuntu_18_04_06.ova Thanks Regards Tilak ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] online freesurfer

External Email - Use Caution Hi: Is there a freesurfer-based system that allows processing online an mprage image? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] WM Hypointensities

External Email - Use Caution Hi Andrew, I can't answer if wm-hypointensity is supported in recon-all-clinical. I'm assuming that you obtained aseg.stats by running mri_segstats. How does your command look like? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On