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
