what does the file transforms/talairach_avi.log say?

and are those pathnames real? or something the email added?

n.

On Wed, 2011-12-28 at 17:08 +0000, LAOUCHEDI MAKHLOUF wrote:

Hi everyone

I run freesurfer recon-all command with the flag -all and I have this error

ERROR:mpr2mni305 failed, see transforms/talairach_avi.log

Some one have any idea?

Thanks

this is the whole process: 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 /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig/001.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tm mri_convert /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/rawavg.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/rawavg.mgz... TR=0.00, 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) Original Data has (1.33, 1, 1) mm size and (128, 256, 256) 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 /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz...

mri_add_xform_to_header -c /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/transforms/talairach.xfm /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_ ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux wn033.grid.scg.nuigalway.ie 2.6.18-274.7.1.el5 #1 SMP Thu Oct 20 15:20:36 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 6559183 exited with ERRORS at Wed Dec 28 16:21:01 GMT 2011

For more details, see the log file /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer