Thanks, it worked.
another question:
i am trying to run tbss on just 2 FA slices of two subjects.
i applied tbss_1_preproc, tbss_2_reg without error message.
The FAi, origdata etc. was created successful.
Now trying to run the third script, i got unfortunately some problems:
i think there are missing some librarys or something like that...
Please could you take a look on the text of the terminal:
[root@localhost mytbss]# tbss_2_reg
[root@localhost mytbss]# tbss_3_postreg
finding best target
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
MARCIO_1_14_FAi 0 0
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
THOMAS_1_10_FAi 0 0
best target is MARCIO_1_14_FAi - now registering this to standard space
affine-registering target to MNI152 space
/usr/local/fsl/bin/DR/areg: error while loading shared libraries:
libstdc++.so.5: cannot open shared object file: No such file or
directory
/usr/local/fsl/bin/DR/transformation: error while loading shared
libraries: libstdc++.so.5: cannot open shared object file: No such file
or directory
transforming (and upsampling) all FA images into MNI152 space
MARCIO_1_14_FAi
/usr/local/fsl/bin/DR/transformation2: error while loading shared
libraries: libstdc++.so.5: cannot open shared object file: No such file
or directory
THOMAS_1_10_FAi
/usr/local/fsl/bin/DR/transformation2: error while loading shared
libraries: libstdc++.so.5: cannot open shared object file: No such file
or directory
merging all upsampled FA images into single 4D image
Usage: avwmerge <-x/y/z/t> <output> <file1 file2 .......>
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
** ERROR: nifti_image_read(all_FA): can't open header file
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Error:: FslCloneHeader: Null pointer passed for FSLIO
creating mean FA
** ERROR: nifti_image_read(all_FA): can't open header file
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
skeletonising mean FA
** ERROR: nifti_image_read(mean_FA): can't open header file
** ERROR: nifti_image_open(mean_FA): bad header info
Error: failed to open file mean_FA
ERROR: Could not open image mean_FA
Image Exception : #22 :: Failed to read volume mean_FA
terminate called after throwing an instance of 'RBD_COMMON::Exception'
/usr/local/fsl/bin/tbss_3_postreg: line 90: 11971 Aborted
${FSLDIR}/bin/tbss_skeleton -i mean_FA -o mean_FA_skeleton
now view mean_FA_skeleton to check whether the default threshold of 2000
needs changing, when running:
tbss_4_prestats [threshold]
[root@localhost mytbss]#
Thanks
Thomas
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