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>
*/Ffôn/*: 02920 879628
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas
N. Greve" <dgr...@mgh.harvard.edu>
*Reply to: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Date: *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>
*/Ffôn/*: 02920 879628
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Reply to: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *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>
*/Ffôn/*: 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>
*/Ffôn/*: 02920 879628
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Reply to: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, 4 May 2020 at 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>
*/Ffôn/*: 02920 879628
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf
of "Douglas N. Greve" <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Reply to: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, 4 May 2020 at 18:54
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Recon-all exited WITH errors
Unfortunately, the log file does not indicate what went
wrong. But it does show that the error happened on the LH
(so it is not just RH). Run the command below and send all
terminal output
cd
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
mris_anatomical_stats -mgz -cortex
../label/lh.cortex.label -f
../stats/lh.aparc.DKTatlas40.stats -b -a
../label/lh.aparc.DKTatlas40.annot -c
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
On 5/4/2020 1:34 PM, Mason Wells wrote:
* External Email - Use Caution *
Hi Experts,
I appear to be having some issues with recon-all. I
ran the command from a bash script (see attached), and
it appears to work fine for the left hemisphere as the
correct files are in the surf folder. However, there
are no right hemisphere surf files. I have attached
the log and error log for PPT01 and PPT02. Any advice
on as to why this has happened would be great.
Thanks in advance,
Mason
*Mason T Wells, MSc*
*PhD student*
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK
*/Email/*: wells...@cardiff.ac.uk
<mailto:wells...@cardiff.ac.uk>
*/Tel/*: 02920 879628
*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->
*Mason T Wells, MSc*
*Myfyriwr PhD*
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol
Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU
*/E-bost/*: wells...@caerdydd.ac.uk
<mailto:wells...@caerdydd.ac.uk>
*/Ffôn/*: 02920 879628
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