Thank you, Zeke for your help! Best wishes, Hisako
-----Original Message----- From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] Sent: Tuesday, August 04, 2015 4:08 PM To: Freesurfer support list; Fujiwara, Hisako Subject: Re: [Freesurfer] recon-all exited with errors Hello Hisako, This is a recently discovered bug either mni related or VirtualBox related. The issue is that the "mri_nu_correct.mni" command will fail when executed in the VirtualBox environment on a subject whose data exists on a shared folder between the host and the virtual machine. Currently, the only known solution is to import the subject data folder into the VirtualBox environment, and then run recon-all. -Zeke On 08/04/2015 11:19 AM, Fujiwara, Hisako wrote: > Hello, > > I am very new to freesurfer who have been using SPM and FSL, and just > started doing individual subject analysis. I already had an error > message on recon-all step. > > I am using: > > Vertualbox, OS is RedHat 64-bit > > I am using bash (I prefer to do so) so I am not in tsch shell. > > The recon-all process was terminated with error but not sure exactly > what the error was even I looked at the recon-all.log file which is > attached to this e-mail. According to the line of script, there should > be a file called 'talairach.xfm in /mri/transforms folder but I see > only the folder called 'bak' which is empty. > > Please advise what is the exact error is and how to solve this problem. > > Thank you so much for your help in advance. > > Hisako > > ***************** > > fsuser@xubuntu-VirtualBox:/media/sf_shared_folder/CAE_MRI$ recon-all > -i CAE_2_1_T1.nii -subject CAE_2_1 -all > > WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! > > Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 > > Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 > > INFO: SUBJECTS_DIR is /media/sf_shared_folder > > Actual FREESURFER_HOME /usr/local/freesurfer > > Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 > 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux > > /media/sf_shared_folder/CAE_2_1 > > mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii > /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz > > mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii > /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz > > INFO: using NIfTI-1 qform > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (0, -1, 0) > > j_ras = (0, 0, -1) > > k_ras = (1, 0, 0) > > writing to /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz... > > #-------------------------------------------- > > #@# MotionCor Tue Aug 4 10:04:50 EDT 2015 > > Found 1 runs > > /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz > > Checking for (invalid) multi-frame inputs... > > WARNING: only one run found. This is OK, but motion > > correction cannot be performed on one run, so I'll > > copy the run to rawavg and continue. > > cp /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz > /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz > > /media/sf_shared_folder/CAE_2_1 > > mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz > /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform > > mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz > /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (0, -1, 0) > > j_ras = (0, 0, -1) > > k_ras = (1, 0, 0) > > Original Data has (0.976562, 0.976562, 1) mm size and (256, 256, 180) > voxels. > > Data is conformed to 1 mm size and 256 voxels for all directions > > changing data type from float to uchar (noscale = 0)... > > MRIchangeType: Building histogram > > Reslicing using trilinear interpolation > > writing to /media/sf_shared_folder/CAE_2_1/mri/orig.mgz... > > mri_add_xform_to_header -c > /media/sf_shared_folder/CAE_2_1/mri/transforms/talairach.xfm > /media/sf_shared_folder/CAE_2_1/mri/orig.mgz > /media/sf_shared_folder/CAE_2_1/mri/orig.mgz > > INFO: extension is mgz > > #-------------------------------------------- > > #@# Talairach Tue Aug 4 10:05:06 EDT 2015 > > /media/sf_shared_folder/CAE_2_1/mri > > mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz > > Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 > 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux > > recon-all -s CAE_2_1 exited with ERRORS at Tue Aug 4 10:05:13 EDT > 2015 > > For more details, see the log file > /media/sf_shared_folder/CAE_2_1/scripts/recon-all.log > > To report a problem, see > https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.har > vard.edu_fswiki_BugReporting&d=BQIF-g&c=P0c35rBvlN7D8BNx7kSJTg&r=irT_w > sJtD80udNn2jMvx1MUsr-k7TAFC5R4iJrY-rOA&m=CNRhBZT-7el4JHrXWT1pMkcCxTr7n > AiwdW0KqdCmL-0&s=77s99nYShDEQhOUBas6lQvd60QUPBdrcqJYMzY93ExM&e= > > fsuser@xubuntu-VirtualBox:/media/sf_shared_folder/CAE_MRI$ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer&d=BQIF-g&c=P0c35rBvlN7D8BNx7kSJTg& > r=irT_wsJtD80udNn2jMvx1MUsr-k7TAFC5R4iJrY-rOA&m=CNRhBZT-7el4JHrXWT1pMk > cCxTr7nAiwdW0KqdCmL-0&s=WVZhU7bJ4kuCeXzBD2HPFCazRtWNHfJlBaX2OeDNp54&e= > The information in this e-mail is intended only for the person to whom it is addressed. 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