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