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/https_3a_2f_2fwms01. ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-47e5- ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/711- 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-5994-47e5- ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/711- 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

if symlinking the long pathname to a shorter one doesnt help, you can also try downloading a set of updates which were rebuilt to include more space for long filenames.

the files for 64b linux are here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64

and are named *4dfp. copy those files to your $FREESURFER_HOME/bin.

n.

On Tue, 2012-01-03 at 16:35 +0000, 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/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/711-2B_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-5994-47e5-ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/711-2C_as_mni_average_305 /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer