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Hello fsl users,
I tried to run sienax with the following options sienax <filename >-d -S "-i 20" -r and an error pops up:
dinos@Spartan:~/Desktop/Alzheimers$ sienax 002_S_0816_AD_M06_reducedFOV -d -S "-i 20" -r
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_1'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_1): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_1
Cannot open volume I_stdmaskbrain_pve_1 for reading!
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_1_segperiph'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_1_segperiph): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_1_segperiph
ERROR: Could not open image I_stdmaskbrain_pve_1_segperiph
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_1_segperiph
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_0'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_0): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_0
Cannot open volume I_stdmaskbrain_pve_0 for reading!
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_0_segvent'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_0_segvent): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_0_segvent
ERROR: Could not open image I_stdmaskbrain_pve_0_segvent
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_0_segvent
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_1'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_1): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_1
ERROR: Could not open image I_stdmaskbrain_pve_1
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_1
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_2'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_2): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_2
ERROR: Could not open image I_stdmaskbrain_pve_2
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_2
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_seg'
** ERROR: nifti_image_open(I_stdmaskbrain_seg): bad header info
ERROR: failed to open file I_stdmaskbrain_seg
ERROR: Could not open image I_stdmaskbrain_seg
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
** ERROR (nifti_image_read): failed to find header file for 'I_render'
** ERROR: nifti_image_open(I_render): bad header info
ERROR: failed to open file I_render
ERROR: Could not open image I_render
Image Exception : #22 :: Failed to read volume I_render
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
Cannot open grIa.png for reading
Segmentation fault
/bin/rm: cannot remove `grI?.???': No such file or directory
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_1_segperiph'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_1_segperiph): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_1_segperiph
ERROR: Could not open image I_stdmaskbrain_pve_1_segperiph
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_1_segperiph
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_0_segvent'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_0_segvent): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_0_segvent
ERROR: Could not open image I_stdmaskbrain_pve_0_segvent
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_0_segvent
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
** ERROR (nifti_image_read): failed to find header file for 'I_periph_render'
** ERROR: nifti_image_open(I_periph_render): bad header info
ERROR: failed to open file I_periph_render
ERROR: Could not open image I_periph_render
Image Exception : #22 :: Failed to read volume I_periph_render
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
Cannot open grIa.png for reading
Segmentation fault
** ERROR (nifti_image_read): failed to find header file for 'I_vent_render'
** ERROR: nifti_image_open(I_vent_render): bad header info
ERROR: failed to open file I_vent_render
ERROR: Could not open image I_vent_render
Image Exception : #22 :: Failed to read volume I_vent_render
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
Cannot open grIa.png for reading
Segmentation fault
/bin/rm: cannot remove `grI?.???': No such file or directory
Finished. The SIENAX report can be viewed by pointing your web browser at:
file:/home/dinos/Desktop/Alzheimers/002_S_0816_AD_M06_reducedFOV_sienax/report.html
Estimated normalised brain volume (NBV) =
2.42
dinos@Spartan:~/Desktop/Alzheimers$ sienax 002_S_0816_AD_M06_reducedFOV.nii.gz -r
Finished. The SIENAX report can be viewed by pointing your web browser at:
file:/home/dinos/Desktop/Alzheimers/002_S_0816_AD_M06_reducedFOV_sienax/report.html
Estimated normalised brain volume (NBV) =
1261092.05
When I leave out the -S "-i 20" the analysis continues normally without errors.
I replicated the same error in another system where fsl was installed by another user than me.
Can you verify this issue as well or there's something wrong in our installations here?
dinos@Spartan:~/Desktop/Alzheimers$ fslerrorreport
/usr/lib/fsl/4.1/fslerrorreport: 92: quota: not found
** ERROR (nifti_image_read): failed to find header file for '/home/dinos/Desktop/Alzheimers'
** ERROR: nifti_image_open(/home/dinos/Desktop/Alzheimers): bad header info
ERROR: failed to open file /home/dinos/Desktop/Alzheimers
ERROR: Could not open file
######################################################################
#### MACHINE INFORMATION
######################################################################
Uname:
Linux
df:
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/sdb2 96124936 37756976 53485004 42% /home
quota:
Memory and Swap info:
MemTotal: 2042796 kB
MemFree: 1155728 kB
Buffers: 21072 kB
Cached: 266512 kB
SwapCached: 7656 kB
Active: 404616 kB
Inactive: 388664 kB
Active(anon): 234188 kB
Inactive(anon): 292492 kB
Active(file): 170428 kB
Inactive(file): 96172 kB
Unevictable: 0 kB
Mlocked: 0 kB
HighTotal: 1169616 kB
HighFree: 407736 kB
LowTotal: 873180 kB
LowFree: 747992 kB
SwapTotal: 9767484 kB
SwapFree: 9636900 kB
Dirty: 64 kB
Writeback: 0 kB
AnonPages: 500028 kB
Mapped: 58912 kB
Shmem: 20860 kB
Slab: 34912 kB
SReclaimable: 21736 kB
SUnreclaim: 13176 kB
KernelStack: 2808 kB
PageTables: 8892 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 10788880 kB
Committed_AS: 3022136 kB
VmallocTotal: 122880 kB
VmallocUsed: 73320 kB
VmallocChunk: 34812 kB
HardwareCorrupted: 0 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 4096 kB
DirectMap4k: 28664 kB
DirectMap4M: 880640 kB
######################################################################
#### ENVIRONMENT INFORMATION
######################################################################
FSLDIR=/usr/share/fsl/4.1
FSLTCLSH=/usr/bin/tclsh
FSLMULTIFILEQUIT=TRUE
FSLMACHINELIST=
FSLOUTPUTTYPE=NIFTI_GZ
FSLBROWSER=/etc/alternatives/x-www-browser
FSLWISH=/usr/bin/wish
FSLREMOTECALL=
FSLLOCKDIR=
LD_LIBRARY_PATH=/usr/lib/fsl/4.1
MANDATORY_PATH=/usr/share/gconf/gnome.mandatory.path
DEFAULTS_PATH=/usr/share/gconf/gnome.default.path
WINDOWPATH=7
PATH=/home/dinos/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/lib/fsl/4.1
LD_LIBRARY_PATH=/usr/lib/fsl/4.1
######################################################################
#### DIRECTORY INFORMATION
######################################################################
PWD:
/home/dinos/Desktop/Alzheimers
total 101496
drwxr-xr-x 5 dinos dinos 4096 2011-10-08 16:38 .
drwxr-xr-x 11 dinos dinos 4096 2011-10-07 15:16 ..
-rw-r--r-- 1 dinos dinos 348 2010-01-20 14:21 002_S_0413_CL_M06.hdr
-rw-r--r-- 1 dinos dinos 43515904 2010-01-20 14:22 002_S_0413_CL_M06.img
-rw-r--r-- 1 dinos dinos 348 2009-12-30 21:44 002_S_0413_CL_SC.hdr
-rw-r--r-- 1 dinos dinos 43515904 2009-12-30 21:44 002_S_0413_CL_SC.img
-rw-r--r-- 1 dinos dinos 16749131 2007-12-11 17:23 002_S_0816_AD_M06_reducedFOV.nii.gz
drwxr-xr-x 2 dinos dinos 4096 2011-10-08 16:51 002_S_0816_AD_M06_reducedFOV_sienax
drwxr-xr-x 4 dinos dinos 4096 2011-10-05 19:58 controls
drwxr-xr-x 2 dinos dinos 4096 2011-10-05 19:36 patients
######################################################################
#### IMAGE INFORMATION
######################################################################
This error report is saved in the file: /tmp/fsl_7oBYKh.gz
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