 |
 |
Hi, I think the problem here is that you do not have write permission in the directory /usr/share/fsl-feeds/examples/ as all the error messages are about files that cannot be written. It seems to read files fine, as indicated by the initial output from FAST. Also, your PATH, as indicated by the fslerrorreport, seems strange as you have /usr/lib/fsl at the end of your PATH but you have fsl installed in /usr/share/fsl according to FSLDIR. However, this is an independent issue, but might be worth fixing as otherwise you may not be able to so easily use the fsl tools. All the best, Mark On 3 Dec 2006, at 01:58, Antonios - Constantine wrote: > Hello fsl users, > > I'm a beginner on fsl, i installed fsl in ubuntu linux platform , > i run > the evaluation tests and everything was ok. > Even though when i tried (to get started with fsl) to run BET > SUSAN FAST > FLIRT with the example images of the fsl -feeds i had the > following errors: > > on BET: > > Error: failed to open file /usr/share/fsl-feeds/examples/ > structural_brain.nii.gz > Error:: FslCloneHeader: Null pointer passed for FSLIO > Finished > > on SUSAN: > > Error: failed to open file /usr/share/fsl-feeds/examples/ > structural_susan.nii.gz > Error:: FslCloneHeader: Null pointer passed for FSLIO > Finished > > on FAST: > > 281091.0 798322.1 556946.9 > FAST - FMRIB's Automated Segmentation Tool Version 3.53 > > Image: /tmp/fsl_Mr9Clb_structural_brain > > T1-weighted image > Imagesize : 256 x 256 x 128 > Pixelsize : 1 x 1 x 2 > > Initial K-means segmentation... > 8 main iterations ... > Estimating PVE... > > Segmentation done successfully! > > Calculation time 250 seconds! > > Write segmentation image /tmp/fsl_Mr9Clb.fastout/QQQQQ_seg.hdr > Successfully! > Write restored image /tmp/fsl_Mr9Clb.fastout/QQQQQ_restore.hdr > Successfully! > Write bias field image /tmp/fsl_Mr9Clb.fastout/QQQQQ_bias.hdr > Successfully! > Write PVE image of tissue 0 Successfully! > Write PVE image of tissue 1 Successfully! > Write PVE image of tissue 2 Successfully! > > Class: CSF tissue 1 tissue 2 brain > percentageVolumes: 0.828222 > Error: failed to open file > /usr/share/fsl-feeds/examples/structural_brain_bias.nii.gz > Error:: FslCloneHeader: Null pointer passed for FSLIO > Error: failed to open file > /usr/share/fsl-feeds/examples/structural_brain_pve_0.nii.gz > Error:: FslCloneHeader: Null pointer passed for FSLIO > Error: failed to open file > /usr/share/fsl-feeds/examples/structural_brain_pve_1.nii.gz > Error:: FslCloneHeader: Null pointer passed for FSLIO > Error: failed to open file > /usr/share/fsl-feeds/examples/structural_brain_pve_2.nii.gz > Error:: FslCloneHeader: Null pointer passed for FSLIO > Error: failed to open file > /usr/share/fsl-feeds/examples/structural_brain_restore.nii.gz > Error:: FslCloneHeader: Null pointer passed for FSLIO > Error: failed to open file > /usr/share/fsl-feeds/examples/structural_brain_seg.nii.gz > Error:: FslCloneHeader: Null pointer passed for FSLIO > Finished > > and finally on FLIRT : > > Could not open file > /usr/share/fsl-feeds/examples/structural_brain2standard.mat for > writing > Error: failed to open file > /usr/share/fsl-feeds/examples/structural_brain2standard.nii.gz > ERROR: Could not open image > /usr/share/fsl-feeds/examples/structural_brain2standard > Image Exception : #23 :: Failed to open volume > /usr/share/fsl-feeds/examples/structural_brain2standard for writing > terminate called after throwing an instance of > 'RBD_COMMON::BaseException' > Finished > > > both images "structural" and "stuctural_brain" looked ok when i > opened them > with fslview > > Can you help me please? > Thanks in advance > > Dinos > > P.S. i also attached the fsl error report > <fsl_ZU5ZO8.gz>