Hi Avi
just running recon-all I think. Is there an env variable you use to specify a tmp dir or something?
thanks Bruce
On Tue, 3 Jan 2012, Snyder, Avi wrote:
It looks like both the command (imgreg_4dfp) and argument (.../711-2B_as_mni_average_305_mask.4dfp.img) fields are garbled. Evidently, operating system paths have not been correctly set. The 4dfp suite of tools is available and probably could be installed but I'm not sure that is what is wanted. I don't understand what LAOUCHEDI MAKHLOUF is trying to do.
AZS
On 1/3/12 10:40 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
this is actually not part of FreeSurfer proper, but rather something that Avi Synder (ccd) was kind enough to contribute. Avi: can you comment?
thanks Bruce On Tue, 3 Jan 2012, LAOUCHEDI MAKHLOUF wrote:
hi everyone we run recon-all on a cloud and we obtained this error:
mpr2mni305 failed, see transforms/talairach_avi.log
The log says the file name is too long perhaps because of the tmp dir file names:
get_4dfp_dimoe:/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/htt ps_3a_2f_2fwms01.
ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-47e 5-
ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/71 1- 2B_as_mni_average_305_mask.4dfp.img filename too long ERROR: 'imgreg_4dfp/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/https_ 3a_2f_2fwms01.
ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-47e 5-
ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/71 1- 2C_as_mni_average_305 /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.i
e/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/ .t
mp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask8201883777111446775 /f reesurfer/average/711-2B_as_mni_average_305_masktalsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=255
knowing that it is difficult for us to do things differently (to change the path); is it possible to do something in freesurfer to work with thesse filenames ?
thanks for your help