External Email - Use Caution Hi,
Terminal output is below: /Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$ mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz... mghRead(/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: [email protected]<mailto:[email protected]> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: [email protected]<mailto:[email protected]> Ffôn: 02920 879628 From: <[email protected]> on behalf of "Douglas N. Greve" <[email protected]> Reply to: Freesurfer support list <[email protected]> Date: Monday, 4 May 2020 at 18:54 To: "[email protected]" <[email protected]> Subject: Re: [Freesurfer] Recon-all exited WITH errors Unfortunately, the log file does not indicate what went wrong. But it does show that the error happened on the LH (so it is not just RH). Run the command below and send all terminal output cd /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white On 5/4/2020 1:34 PM, Mason Wells wrote: External Email - Use Caution Hi Experts, I appear to be having some issues with recon-all. I ran the command from a bash script (see attached), and it appears to work fine for the left hemisphere as the correct files are in the surf folder. However, there are no right hemisphere surf files. I have attached the log and error log for PPT01 and PPT02. Any advice on as to why this has happened would be great. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: [email protected]<mailto:[email protected]> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: [email protected]<mailto:[email protected]> Ffôn: 02920 879628 _______________________________________________ Freesurfer mailing list [email protected]<mailto:[email protected]> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Ca34c68367384408ae1b108d7f0543691%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637242116792959065&sdata=M%2FrDXvQDAM8qFf6QIqF6vx9m%2Bp1M65%2Bv79rhH1hatHA%3D&reserved=0>
_______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
