External Email - Use Caution Hi Doug,
Not sure if my email below got to you? I sent the terminal outputs of the command you told me to run. Any idea what’s going on or how to fix it? 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: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk> 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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk> Ffôn: 02920 879628 From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mason Wells <wells...@cardiff.ac.uk> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Monday, 4 May 2020 at 20:01 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed} External Email - Use Caution Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below: 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 /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz... reading input surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white... reading input pial surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial... reading input white surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white... reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1698 1132 3274 2.730 0.526 0.130 0.032 26 2.4 caudalanteriorcingulate 4375 2908 8369 2.594 0.599 0.127 0.040 46 7.0 caudalmiddlefrontal 3883 2464 5378 2.087 0.498 0.149 0.082 74 9.4 cuneus 546 373 1423 2.817 0.999 0.154 0.087 11 1.9 entorhinal 5411 3506 10979 2.768 0.567 0.137 0.059 101 14.8 fusiform 6159 4159 11629 2.543 0.520 0.133 0.045 86 11.0 inferiorparietal 5973 3945 13736 2.965 0.705 0.138 0.060 130 13.4 inferiortemporal 1536 934 2788 2.725 0.838 0.164 0.090 50 5.1 isthmuscingulate 6953 4476 11030 2.320 0.542 0.147 0.055 110 15.3 lateraloccipital 3897 2512 7780 2.641 0.630 0.147 0.077 99 13.1 lateralorbitofrontal 5273 3237 7567 2.161 0.603 0.151 0.956 191 20.8 lingual 2015 1290 4210 2.576 0.773 0.157 0.084 64 6.5 medialorbitofrontal 6073 4091 14456 3.026 0.553 0.130 0.043 80 11.0 middletemporal 1012 711 2254 2.886 0.735 0.133 0.112 16 6.3 parahippocampal 2182 1401 4296 2.690 0.669 0.128 0.044 26 4.5 paracentral 3247 2175 6722 2.682 0.501 0.121 0.038 34 5.1 parsopercularis 1195 793 2520 2.549 0.514 0.138 0.045 21 2.1 parsorbitalis 2780 1882 5377 2.457 0.608 0.131 0.043 37 5.0 parstriangularis 2229 1444 2359 1.685 0.476 0.155 0.067 41 6.1 pericalcarine 7692 4818 11728 2.218 0.657 0.130 0.053 114 16.0 postcentral 1983 1360 4109 2.902 0.617 0.167 0.079 44 6.1 posteriorcingulate 7681 4765 13220 2.521 0.549 0.123 0.056 119 15.1 precentral 6240 4189 11573 2.532 0.576 0.145 0.052 104 13.3 precuneus 1613 992 3166 2.820 0.661 0.136 0.055 54 3.6 rostralanteriorcingulate 6644 4495 12118 2.347 0.579 0.144 0.052 117 13.9 rostralmiddlefrontal 12967 8768 28469 2.839 0.612 0.132 0.047 170 25.1 superiorfrontal 7963 5213 12201 2.095 0.481 0.125 0.053 125 16.2 superiorparietal 9021 6069 20753 3.059 0.612 0.130 0.050 183 19.9 superiortemporal 7970 5269 15543 2.684 0.502 0.149 0.074 910 17.4 supramarginal 702 454 1432 2.844 0.618 0.133 0.046 8 1.3 transversetemporal 2953 1947 6539 3.228 0.801 0.124 0.056 33 6.4 insula 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: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk> 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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk> Ffôn: 02920 879628 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: Monday, 4 May 2020 at 19:56 To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed} Something else has gone wrong. wm.mgz should have been there in order to get as far as it did. Is your SUBJECTS_DIR set properly? On 5/4/2020 2:49 PM, Mason Wells wrote: 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: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk> 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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk> Ffôn: 02920 879628 From: <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> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, 4 May 2020 at 18:54 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] 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: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk> 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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk> Ffôn: 02920 879628 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be 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%7Cc2e001d423454cc92a6008d7f05d82c6%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637242156732809583&sdata=s8UPm0sywZKp0bHkmS3g4ifNdHSTHxr0LhuA4gn0mbA%3D&reserved=0> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be 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%7Cc2e001d423454cc92a6008d7f05d82c6%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637242156732809583&sdata=s8UPm0sywZKp0bHkmS3g4ifNdHSTHxr0LhuA4gn0mbA%3D&reserved=0>
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