No special procedures come to mind. You can use mri_segstats using the PVC'ed PET image as input and aux/seg.nii.gz as the segmentation and aux/seg.ctab as the colortable.
On 5/7/2020 1:31 PM, Ferraro, Pilar wrote: > External Email - Use Caution > > Dear Freesurfer experts, > > As previously mentioned, we are currently trying to test the effects of > different PVC corrections on metabolism estimation in a group of patients. > > We would like to also include MZ and MG methods in the analyses, comparing > them to SGTM and no PVC. > However, while both MG and MZ provide voxel-wise results, we would like to > use them in ROI analyses in order to be able to compare their outputs with > the ones obtained with SGTM and no PVC. > Are there any procedures that you would recommend to do this? > > Many thanks in advance for any help, > > Best, > > Pilar > > > >> Il giorno 7 mag 2020, alle ore 6:00 PM, >> freesurfer-requ...@nmr.mgh.harvard.edu ha scritto: >> >> Send Freesurfer mailing list submissions to >> freesurfer@nmr.mgh.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> or, via email, send a message with subject or body 'help' to >> freesurfer-requ...@nmr.mgh.harvard.edu >> >> You can reach the person managing the list at >> freesurfer-ow...@nmr.mgh.harvard.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Freesurfer digest..." >> >> >> Today's Topics: >> >> 1. Re: HCPMMP1 parcellation to aseg (.mgz) (pooja prabhu) >> 2. Re: HCPMMP1 parcellation to aseg (.mgz) (Douglas N. Greve) >> 3. Re: Recon-all exited WITH errors {Disarmed} (Mason Wells) >> 4. Re: freesurfer 7.0.0 in a virtual machine... (Gonzalo Rojas Costa) >> 5. Re: Recon-all exited WITH errors {Disarmed} (Douglas N. Greve) >> 6. Re: flirt.fsl error (NEWMAT::SingularException) when running >> bbregister in Freesurfer 7.0.0 (Hoopes, Andrew) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 7 May 2020 20:55:21 +0530 >> From: pooja prabhu <prabhuppo...@gmail.com> >> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz) >> To: freesurfer@nmr.mgh.harvard.edu >> Message-ID: >> <caneoyknobqgkppsdx+pr1cmvhrye2d+zirvemfz9bqj4-rs...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> External Email - Use Caution >> >> HCPMMP1 parcellation is multi modal parcellation >> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/ >> >> We need the file something like we have for 'aparc' parcellation. >> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz) >> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot) >> >> -- >> Thank You >> Pooja Prabhu >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200507/a041a4a6/attachment-0001.html >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 7 May 2020 11:26:14 -0400 >> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> >> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz) >> To: <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <01355b15-25bd-9a44-2d75-e2eefe70a...@mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> sorry, can you include the previous emails? >> >> On 5/7/2020 11:25 AM, pooja prabhu wrote: >>> ????????External Email - Use Caution >>> >>> HCPMMP1 parcellation is multi modal parcellation >>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/ >>> >>> We need the file something like we have for 'aparc' parcellation. >>> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz) >>> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot) >>> >>> -- >>> Thank You >>> Pooja Prabhu >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200507/86de4fd9/attachment-0001.html >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 7 May 2020 15:33:26 +0000 >> From: Mason Wells <wells...@cardiff.ac.uk> >> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed} >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <d4803927-b60a-40d9-840e-b0201a6fb...@cardiff.ac.uk> >> Content-Type: text/plain; charset="utf-8" >> >> External Email - Use Caution >> >> Terminal output is below: >> >> >> export >> SUBJECTS_DIR=/home/c1749990/Documents/Analysis/Data/freesurfer/subjects >> >> c1749990@l029:~/Documents/Analysis/Data/PMA_retinoScans/PPT_004$ recon-all >> -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3 -label_v1 >> recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3 -label_v1 >> >> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> INFO: SUBJECTS_DIR is >> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects >> Actual FREESURFER_HOME /cubric/software/freesurfer.versions/5.3.0 >> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr 29 >> 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux >> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004 >> >> mri_convert >> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz >> >> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz >> >> mri_convert >> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz >> >> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from >> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz... >> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, 0, 0) >> j_ras = (0, 1, 0) >> k_ras = (0, 0, 1) >> writing to >> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz... >> #----------------------------------------- >> #@# Parcellation Stats 3 lh Thu May 7 16:32:30 BST 2020 >> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/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_004 lh white >> >> No such file or directory >> mris_anatomical_stats: could not open label file ../label/lh.cortex.label >> INFO: assuming MGZ format for volumes. >> Invalid argument >> >> Invalid argument >> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr 29 >> 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s PPT_004 exited with ERRORS at Thu May 7 16:32:30 BST 2020 >> >> For more details, see the log file >> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts/recon-all.log >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> 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> >> Ff?n: 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: Thursday, 7 May 2020 at 15:59 >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed} >> >> No all, just one. And try running it with just the -parcstats3 flag (ie, >> don't use -all or -autreconX). You should have an answer in seconds >> On 5/7/2020 7:50 AM, Mason Wells wrote: >> >> External Email - Use Caution >> Hi Doug, >> >> Sorry I am a bit confused. I ran recon-all as a bash for 30 participants. >> None of which had the right hemisphere completed and recon-all log says >> exited with errors (as the log in the original email shows). Are you >> suggesting I go back and re-run recon-all via the bash and see if I get the >> same issue? >> >> Thanks for all your help. >> 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> >> Ff?n: 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: Wednesday, 6 May 2020 at 23:11 >> 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 >> >> It looks like that command finished without error. Have you tried running it >> in recon-all again to see if it fails again? You can just run that command >> with -parcstats3 >> >> >> On 5/6/2020 6:41 AM, Mason Wells wrote: >> >> 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> >> Ff?n: 02920 879628 >> >> >> From: >> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> on behalf of Mason Wells >> <wells...@cardiff.ac.uk><mailto:wells...@cardiff.ac.uk> >> Reply to: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> >> Date: Monday, 4 May 2020 at 20:01 >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu><mailto: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> >> Ff?n: 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 19:56 >> 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 {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> >> Ff?n: 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> >> Ff?n: 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%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426581476&sdata=9FzX4UxRBUrO5onyn1ZwE7pjqrUEv5WMHV1MB1u1%2FG8%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%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426581476&sdata=9FzX4UxRBUrO5onyn1ZwE7pjqrUEv5WMHV1MB1u1%2FG8%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%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426591477&sdata=KRIOcP2dXJl7bJbUCXXRpgTBoji0jSteH5S5oT7YZcc%3D&reserved=0> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> 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%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426601472&sdata=fXDymBlzoXir0xwsk4dREaQs1r7YWliUKBnK2sV%2B49c%3D&reserved=0> >> >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200507/f3b9f4a0/attachment-0001.html >> >> ------------------------------ >> >> Message: 4 >> Date: Thu, 7 May 2020 15:34:37 -0400 >> From: Gonzalo Rojas Costa <gonzalo.rojas.co...@gmail.com> >> Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine... >> To: ts...@rcmd.org >> Cc: freesurfer@nmr.mgh.harvard.edu >> Message-ID: >> <CAHPHMw7tiFRNOL=qSddTQr-z6b=nuqE7ZMvBV7tq=gbrzmi...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> External Email - Use Caution >> >> Hi: >> >> No... I don't have any specific issue... I have a previous freesurfer >> version installed that I want to continue using. So I want to install >> version freesurfer 7.0 on a virtual machine... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >>> Message: 4 >>> Date: Thu, 7 May 2020 12:43:56 +0200 (CEST) >>> From: Tim Sch?fer <ts...@rcmd.org> >>> Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine... >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <1445340988.123994.1588848236...@ox.hosteurope.de> >>> Content-Type: text/plain; charset="utf-8" >>> >>> External Email - Use Caution >>> >>> There should be no difference to installation on a physical machine. Are >> you >>> running into any specific issues? >>> >>> Tim >>> >>>> On May 7, 2020 at 3:51 AM Gonzalo Rojas Costa < >> gonzalo.rojas.co...@gmail.com> wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Hi: >>>> >>>> How can install freesurfer 7.0.0 in a virtual machine ? >>>> >>>> Sincerely, >>>> >>>> >>>> Gonzalo Rojas Costa >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Dr. Tim Sch?fer >>> Postdoc Computational Neuroimaging >>> Department of Child and Adolescent Psychiatry, Psychosomatics and >>> Psychotherapy >>> University Hospital Frankfurt, Goethe University Frankfurt am Main, >> Germany >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200507/1afb9df5/attachment-0001.html >> >> ------------------------------ >> >> Message: 5 >> Date: Thu, 7 May 2020 11:47:15 -0400 >> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> >> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed} >> To: <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <f05dbd88-2bbd-775e-6a11-38c285834...@mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> Does >> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/label/lh.cortex.label >> exist? >> >> On 5/7/2020 11:33 AM, Mason Wells wrote: >>> ????????External Email - Use Caution >>> >>> Terminal output is below: >>> >>> export >>> SUBJECTS_DIR=/home/c1749990/Documents/Analysis/Data/freesurfer/subjects >>> >>> c1749990@l029:~/Documents/Analysis/Data/PMA_retinoScans/PPT_004$ >>> recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3 >>> -label_v1 >>> >>> recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3 >>> -label_v1 >>> >>> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >>> >>> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >>> >>> INFO: SUBJECTS_DIR is >>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects >>> >>> Actual FREESURFER_HOME /cubric/software/freesurfer.versions/5.3.0 >>> >>> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr >>> 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux >>> >>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004 >>> >>> mri_convert >>> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz >>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz >>> >>> >>> mri_convert >>> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz >>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz >>> >>> >>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >>> >>> reading from >>> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz... >>> >>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 >>> >>> i_ras = (-1, 0, 0) >>> >>> j_ras = (0, 1, 0) >>> >>> k_ras = (0, 0, 1) >>> >>> writing to >>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz... >>> >>> #----------------------------------------- >>> >>> #@# Parcellation Stats 3 lh Thu May? 7 16:32:30 BST 2020 >>> >>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/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_004 lh white >>> >>> No such file or directory >>> >>> mris_anatomical_stats: could not open label file ../label/lh.cortex.label >>> >>> INFO: assuming MGZ format for volumes. >>> >>> Invalid argument >>> >>> Invalid argument >>> >>> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr >>> 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux >>> >>> recon-all -s PPT_004 exited with ERRORS at Thu May? 7 16:32:30 BST 2020 >>> >>> For more details, see the log file >>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts/recon-all.log >>> >>> To report a problem, see >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> >>> *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> >>> >>> */Ff?n/*: 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: *Thursday, 7 May 2020 at 15:59 >>> *To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>> *Subject: *Re: [Freesurfer] Recon-all exited WITH errors {Disarmed} >>> >>> No all, just one. And try running it with just the -parcstats3 flag >>> (ie, don't use -all or -autreconX). You should have an answer in seconds >>> >>> On 5/7/2020 7:50 AM, Mason Wells wrote: >>> >>> *????????External Email - Use Caution * >>> >>> Hi Doug, >>> >>> Sorry I am a bit confused. I ran recon-all as a bash for 30 >>> participants. None of which had the right hemisphere completed and >>> recon-all log says exited with errors (as the log in the original >>> email shows). Are you suggesting I go back and re-run recon-all >>> via the bash and see if I get the same issue? >>> >>> Thanks for all your help. >>> >>> 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> >>> >>> */Ff?n/*: 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: *Wednesday, 6 May 2020 at 23:11 >>> *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 >>> >>> It looks like that command finished without error. Have you tried >>> running it in recon-all again to see if it fails again? You can >>> just run that command with -parcstats3 >>> >>> >>> On 5/6/2020 6:41 AM, Mason Wells wrote: >>> >>> *????????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> >>> >>> */Ff?n/*: 02920 879628 >>> >>> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of >>> Mason Wells <wells...@cardiff.ac.uk> >>> <mailto:wells...@cardiff.ac.uk> >>> *Reply to: *Freesurfer support list >>> <freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> *Date: *Monday, 4 May 2020 at 20:01 >>> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> <mailto: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> >>> >>> */Ff?n/*: 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 19:56 >>> *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 >>> {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> >>> >>> */Ff?n/*: 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> >>> >>> */Ff?n/*: 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%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426581476&sdata=9FzX4UxRBUrO5onyn1ZwE7pjqrUEv5WMHV1MB1u1%2FG8%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%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426581476&sdata=9FzX4UxRBUrO5onyn1ZwE7pjqrUEv5WMHV1MB1u1%2FG8%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%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426591477&sdata=KRIOcP2dXJl7bJbUCXXRpgTBoji0jSteH5S5oT7YZcc%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%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426601472&sdata=fXDymBlzoXir0xwsk4dREaQs1r7YWliUKBnK2sV%2B49c%3D&reserved=0> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200507/b7629997/attachment-0001.html >> >> ------------------------------ >> >> Message: 6 >> Date: Thu, 7 May 2020 15:50:26 +0000 >> From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> >> Subject: Re: [Freesurfer] flirt.fsl error (NEWMAT::SingularException) >> when running bbregister in Freesurfer 7.0.0 >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <ebca186e-5fd0-47ba-95c3-3d80252ac...@mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Julien, >> >> Just to test something out, can you try running this again after replacing >> the flirt.fsl binary in your new 7.0 install with the flirt.fsl binary from >> 6.0? i.e. >> >> cp /path/to/freesurfer/6.0.0/bin/flirst.fsl >> /path/to/freesurfer/7.0.0/bin/flirst.fsl >> >> Let me know how that works. >> >> Best >> Andrew >> >> >> ?On 5/7/20, 8:04 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >> julienbesle" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >> julienbe...@gmail.com> wrote: >> >> External Email - Use Caution >> >> Hi, >> >> I just installed freesurfer v7 and I'm getting an error in a script that >> calls bbregister with the --fslmat and --init-fsl options. This error >> does not occur in freesurfer v6 even when using exactly the same data, >> but it does also occur with a development version of freesurfer I >> downloaded in Sept 2019 (exact same error). >> >> The call is: >> >> DEBUG : 2020-05-06 12:07:12,816 : runCmd : Running: bbregister >> --s HLOSS_p5 --mov >> >> /home/julien/data/HLOSS/pilot05_B/DWI/B0_corrected_mean_resampled_MPRAGE.nii >> --reg >> /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.dat >> --fslmat >> /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.mat >> --init-fsl --dti >> >> The error occurs when bbregister calls fsl.flirt: >> >> INFO : 2020-05-06 12:08:24,560 : main : flirt.fsl -ref >> >> /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii >> -in >> >> /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii >> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 >> -searchrz -90 90 -verbose 0 -omat >> >> /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat >> -schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init >> >> /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat0 >> INFO : 2020-05-06 12:08:55,102 : main : Wed May 6 12:08:54 >> EEST 2020 >> INFO : 2020-05-06 12:08:55,603 : main : /mnt/f/data/HLOSS >> INFO : 2020-05-06 12:08:56,105 : main : flirt.fsl -ref >> >> /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii >> -in >> >> /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii >> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 >> -searchrz -90 90 -verbose 0 -omat >> >> /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat >> -init >> >> /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat >> -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch >> INFO : 2020-05-06 12:09:15,632 : main : terminate called after >> throwing an instance of 'NEWMAT::SingularException' >> INFO : 2020-05-06 12:09:15,633 : main : Abort (core dumped) >> INFO : 2020-05-06 12:09:15,634 : main : ERROR: flirt >> CRITICAL : 2020-05-06 12:09:15,634 : runCmd : Return Value: 1 >> >> It looks like the first time flirt.fsl is called everything goes fine, >> but the second time, the error occurs. Unfortunately this is not a >> script I wrote myself, so I'm not sure what this particular call to >> bbregister is supposed to achieve. I'm not sure the call to fsl.flirt >> depends on which version of FSL I have installed, but just in case, I >> used the FSL v6 and didn't change anything to the FSL installation >> between trying Freesurfer v6, dev or v7. I run everything on Ubuntu >> 16.04 running on WSL on Windows 10. >> >> Any idea what could be going wrong? >> >> Thanks >> >> Julien >> >> -- >> ------------------------------------- >> Julien Besle >> Lagos Center, Apt 9A >> Sadat Street >> Beirut >> Lebanon >> >> tel: +961 78 980 317 >> ------------------------------------- >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> End of Freesurfer Digest, Vol 195, Issue 24 >> ******************************************* > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
