Dear freesurfer experts,
I am running freesurfer “freesurfer-Linux-centos7_x86_64-dev-20150728”. On a Linux terminal: “Linux cortical 3.16.6-2-default #1 SMP Mon Oct 20 13:47:22 UTC 2014 (feb42ea) x86_64 x86_64 x86_64 GNU/Linux” After normal processing of the data cross sectional. Followed by the creation of the within-subject template (DTprae_P01) I get an error message running the longitudinal command (-long). The command line I used was: recon-all -long DTprae_P01 DT_P01 -all
The subject directory is: /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT
The subprocess ending with the error and the error message were the following: mri_fuse_segmentations -a aseg.presurf.mgz -c aseg.auto_noCCseg.mgz -n norm.mgz DTprae_P01.long.DT_P01 DTprae_P01 DTpost_P01 aseg.fused.mgz
mghRead(/mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01/mri/aseg.presurf.mgz, -1): could not open file using aseg.presurf.mgz as aseg volume using aseg.auto_noCCseg.mgz as aseg no-CC-label volume using norm.mgz as norm volume reading /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01.long.DT_P01/mri/norm.mgz and processing 2 timepoints, writing to aseg.fused.mgz loading data for subject DTprae_P01 ... mri_fuse_segmentations: could not read input volume /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01/mri/aseg.presurf.mgz Linux cortical 3.16.6-2-default #1 SMP Mon Oct 20 13:47:22 UTC 2014 (feb42ea) x86_64 x86_64 x86_64 GNU/Linux
recon-all -s DTprae_P01.long.DT_P01 exited with ERRORS at Tue Mar 8 17:52:40 CET 2016
I checked the folder (DTprae_P01/mri) and there is no data called aseg.presurf.mgz. in which step is this data produced? How can I fix this problem?
I hope you could help me. Kind regards,
Sandra
Hi Sandra,
you are running an old dev version from last summer. Who know what is going on in that version of FreeSurfer.
But, I think more likely this is an IO problem on your system. I would recommend to run this specific subject from scratch (cross , base, long). After cross check if this file exists. It should be there. Maybe you ran the cross with an older version of freesurfer?
Martin
On 03/10/2016 09:04 AM, Sandra Preißler wrote:
Dear freesurfer experts,
I am running freesurfer “freesurfer-Linux-centos7_x86_64-dev-20150728”. On a Linux terminal: “Linux cortical 3.16.6-2-default #1 SMP Mon Oct 20 13:47:22 UTC 2014 (feb42ea) x86_64 x86_64 x86_64 GNU/Linux” After normal processing of the data cross sectional. Followed by the creation of the within-subject template (DTprae_P01) I get an error message running the longitudinal command (-long). The command line I used was: recon-all -long DTprae_P01 DT_P01 -all
The subject directory is: /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT
The subprocess ending with the error and the error message were the following: mri_fuse_segmentations -a aseg.presurf.mgz -c aseg.auto_noCCseg.mgz -n norm.mgz DTprae_P01.long.DT_P01 DTprae_P01 DTpost_P01 aseg.fused.mgz
mghRead(/mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01/mri/aseg.presurf.mgz, -1): could not open file using aseg.presurf.mgz as aseg volume using aseg.auto_noCCseg.mgz as aseg no-CC-label volume using norm.mgz as norm volume reading /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01.long.DT_P01/mri/norm.mgz and processing 2 timepoints, writing to aseg.fused.mgz loading data for subject DTprae_P01 ... mri_fuse_segmentations: could not read input volume /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01/mri/aseg.presurf.mgz Linux cortical 3.16.6-2-default #1 SMP Mon Oct 20 13:47:22 UTC 2014 (feb42ea) x86_64 x86_64 x86_64 GNU/Linux
recon-all -s DTprae_P01.long.DT_P01 exited with ERRORS at Tue Mar 8 17:52:40 CET 2016
I checked the folder (DTprae_P01/mri) and there is no data called aseg.presurf.mgz. in which step is this data produced? How can I fix this problem?
I hope you could help me. Kind regards,
Sandra
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Martin Reuter -
Sandra Preißler