Christina,
Glad to hear you fixed the Ubuntu installation. About the feeds test, it seems that some files are not present (from the look of those errors). What feeds test package have you used? I have not run the feeds test in a while (since i installed FSL 2+ years ago),
but if you give me the version number, i can try to see if the problem gets replicated on my computer (one of these days)...
Actually, i see from your first message on April 06 that
"
christina@ubuntu:~/Desktop/feeds$ /usr/bin/time ./RUN all
FSL Evaluation and Example Data Suite v4.1.9
Warning - FSL version (4.1.4) not the same as this test
suite version (4.1.9)! Therefore this test may
not run...maybe you should download the latest version of
the test suite and/or FSL.
"
so the problem may be that you are trying to run tests devised for a newer version of FSL
(hence the missing files, if that is indeed the problem)
Since you have installed FSL - 4.1.4, you should look out for the feeds data pack with the
same version and see if that one fails...
I do have a copy of the old 4.1.4 feeds archive:
$ md5sum fsl-4.1.4-feeds.tar.gz
d8c5f1842442d7dc972c66e5dcc847ec fsl-4.1.4-feeds.tar.gz
Do you want me to send it to you with
www.dropsend.com ? (or you could pick another
free service of the sort, i did a google search and ran into this one)
The other option would be to install the new FSL and try it with the 4.1.9 feeds... (the new
version of Ubuntu-LTS, 12.04 should be available soon anyway and i will also try to install the
new FSL on that one when the time comes).
Let me know what you want me to do (send old feeds / try old FSL distribution with feeds-4.1.9 / nothing).
Silviu
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
