[Freesurfer] Recon-all error message

Dear Freesurfers, I had the following error message while I was running recon-all: Reading curvature file /Data/MRI/002_S_1155-S178671/surf/lh./Data/MRI/002_S_1155-S178671/surf/lh.white.K MRISreadCurvature: could not open Data/MRI/002_S_1155-S178671/surf/lh./Data/MRI/ 002_S_1155-S178671/surf/

Re: [Freesurfer] lGI mris_fill Error

Thank you so much for this suggestion. It worked perfectly. I really appreciate all of your help- with this and the previous question. Best, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical Scho

Re: [Freesurfer] lGI mris_fill Error

Hi Arkadiy, This might have to do with SIP, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ Andrew On Oct 27, 2017, at 2:13 PM, Maksimovskiy, Ark

[Freesurfer] XL Defect Correction

Dear Freesurfer experts, During my recon-all I encountered a problem for one of my subjects, where the process got stalled at "CORRECTING DEFECT 12 (vertices=21293, convex hull=1791) XL defect detected...". I've checked the output and it seems that skull-stripping hasn't been performed prope

[Freesurfer] lGI mris_fill Error

Dear LGI Experts, I am attempting to run LGI using the freesurfer Dev Version (2017), and am getting the following error: [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] amaksimovskiy% recon-all -s SUBJ002 -localGI INFO: FreeSurfer build stamps do not match Su

[Freesurfer] significant of long_mris_slopes

Dear freesurfer group, Hi! I used long_stats_slopes and code to process my longitudinal data: long_stats_slopes --qdec sub_qdec_long.dat --stats lh.aparc.stats --meas thickness --sd $SUBJECTS_DIR --do-rate --generic-time --stack-rate thickness.lh.aparc-rate.stack.txt mri_glmfit --osgm --glmdir thi

Re: [Freesurfer] segmentHA znzread failed error

Thank you so much for your help with this. Much appreciated, * Arkadiy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the p

[Freesurfer] recon-all on previously segmented volumes

Hi, I’m having some issues generating surfaces for an individual and was hoping that a combination of tools might help. In this particular individual, the skull stripping went fine, but a fairly large proportion of the anterior temporal cortex (primarily inferior) volume is excluded from the dat