Dear Michael and Silviu,
thank you for your help!! - I managed to remove the partition and now there are only Windows XP and Ubuntu 10.04 (and swap) left, both systems now have about 40 GB.
I also tried df -h and everything seems to be alright:
Dateisystem Größe Benut Verf Ben% Eingehängt auf
/dev/sda6 37G 5,4G 30G 16% /
none 240M 280K 240M 1% /dev
none 245M 312K 244M 1% /dev/shm
none 245M 84K 245M 1% /var/run
none 245M 0 245M 0% /var/lock
none 245M 0 245M 0% /lib/init/rw
I also downloaded feeds the way you explained it and FAST still fails (but FIRST is alright now):
Starting SIENAX (including testing BET and FLIRT and FAST) at Mo 16. Apr 22:11:09 CEST 2012
checking error on BET:
% error = 0.0
checking error on FLIRT:
% error = 0.03
checking error on FAST:
checking error on single-image binary segmentation:
No output image created
Warning - test failed!
checking error on partial volume images:
No output image created
Warning - test failed!
No output image created
Warning - test failed!
No output image created
Warning - test failed!
checking error on SIENAX volume outputs:
% error = 42.5
Warning - test failed!
% error = 2.65
Warning - test failed!
% error = 53.06
Warning - test failed!
% error = 42.64
Warning - test failed!
% error = 95.71
Warning - test failed!
I tried again cat /tmp/fsl-selftest.7PBmFZ/results/LOG
/usr/share/fsl/4.1/bin/imcp /tmp/fsl-selftest.7PBmFZ/data/structural /tmp/fsl-selftest.7PBmFZ/results/structural
cd /tmp/fsl-selftest.7PBmFZ/results ; /usr/share/fsl/4.1/bin/sienax structural -d -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: Entfernen von „grI?.???“ nicht möglich: Datei oder Verzeichnis nicht gefunden
** 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: Entfernen von „grI?.???“ nicht möglich: Datei oder Verzeichnis nicht gefunden
Finished. The SIENAX report can be viewed by pointing your web browser at:
file:/tmp/fsl-selftest.7PBmFZ/results/structural_sienax/report.html
Estimated normalised brain volume (NBV) =
2.38
And then:
ls -l /tmp/fsl-selftest.7PBmFZ
insgesamt 4
lrwxrwxrwx 1 christina christina 25 2012-04-16 22:11 data -> /usr/share/fsl-feeds/data
drwxr-xr-x 3 christina christina 4096 2012-04-16 22:22 results
lrwxrwxrwx 1 christina christina 24 2012-04-16 22:11 RUN -> /usr/share/fsl-feeds/RUN
ls -l /tmp/fsl-selftest.7PBmFZ/results
insgesamt 13220
-rw-r--r-- 1 christina christina 36769 2012-04-16 22:22 errsq.nii.gz
-rw-r--r-- 1 christina christina 5182 2012-04-16 22:22 LOG
-rw-r--r-- 1 christina christina 78653 2012-04-16 22:22 meansq.nii.gz
-rw-r--r-- 1 christina christina 13404884 2012-04-16 22:11 structural.nii.gz
drwxr-xr-x 2 christina christina 4096 2012-04-16 22:17 structural_sienax
ls -l /tmp/fsl-selftest.7PBmFZ/results/structural_sienax
insgesamt 18268
-rw-r--r-- 1 christina christina 730 2012-04-16 22:16 I2std.avscale
-rw-r--r-- 1 christina christina 141 2012-04-16 22:17 I2std_inv.mat
-rw-r--r-- 1 christina christina 143 2012-04-16 22:16 I2std.mat
-rw-r--r-- 1 christina christina 39744 2012-04-16 22:17 I2std.png
-rw-r--r-- 1 christina christina 190988 2012-04-16 22:11 I_bet.png
-rw-r--r-- 1 christina christina 52668 2012-04-16 22:11 I_brain_mask.nii.gz
-rw-r--r-- 1 christina christina 2231783 2012-04-16 22:11 I_brain.nii.gz
-rw-r--r-- 1 christina christina 87366 2012-04-16 22:11 I_brain_skull.nii.gz
-rw-r--r-- 1 christina christina 225993 2012-04-16 22:17 I_masks.png
-rw-r--r-- 1 christina christina 13404884 2012-04-16 22:11 I.nii.gz
-rw-r--r-- 1 christina christina 2219451 2012-04-16 22:17 I_stdmaskbrain.nii.gz
-rw-r--r-- 1 christina christina 78689 2012-04-16 22:17 I_stdmask.nii.gz
-rw-r--r-- 1 christina christina 88150 2012-04-16 22:17 I_stdmask_segperiph.nii.gz
-rw-r--r-- 1 christina christina 43023 2012-04-16 22:17 I_stdmask_segvent.nii.gz
-rw-r--r-- 1 christina christina 4132 2012-04-16 22:22 report.html
-rw-r--r-- 1 christina christina 905 2012-04-16 22:22 report.sienax
Christina
