Hi, I’ve tried this script in both freesurfer6.0.0 and freesurfer7.1.1, and get the same error message in both. My subjects were processed through recon-all with freesurfer 6.0.0.
Thank you! From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Friday, November 6, 2020 at 10:11 AM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mris_anatomical_stats error: stating file which version of FS are you using? On 11/5/2020 11:29 AM, Chan, Shi Yu wrote: Hi, Yes, sorry! I copied the error message from terminal, but copied the command from my script so I copied the error message for the wrong hemisphere. I apologise for the confusion. I've attached the terminal output (I've put ##### at the lines above the error message) and the script I use in this email. Thank you for all your help! ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Thursday, November 5, 2020 9:44 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mris_anatomical_stats error: stating file Is that the right error msg? It says it can't find the RH, but you are running it with LH. Can you post the entire terminal output? On 11/3/2020 2:00 PM, Chan, Shi Yu wrote: Hi FreeSurfer Developers, I'm trying to calculate cortical thickness statistics from the Yeo 17 Network cortical parcellation and have used mri_surf2surf to get the .annot files for each subject. However, when I run mris_anatomical_stats, I get an error: ERROR: stating file subjects_dir/sub-001/label/sub-001/label/rh.Yeo2011_17Networks_N1000.annot It seems like the "sub-001/label" portion is repeated. The command I use for mris_anatomical_stats is: mris_anatomical_stats -th3 -mgz -cortex sub-001/label/lh.cortex.label -f sub-001/stats/lh.Yeo_17Networks.stats -b -a sub-001/label/lh.Yeo2011_17Networks_N1000.annot sub-001 lh white The command still runs despite the error, and outputs the stats files accordingly, so I'm not sure how important this error is, but I can't figure out how to fix it. This is a similar issue to: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67595.html but I've checked $SUBJECTS_DIR, and it is correct. If I run ls $SUBJECTS_DIR/sub-001 I'll see all the different sub-folders in sub-001 (mri stats labels etc) Any help would be much appreciated! Thank you! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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