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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| November 06, 2008 02:17PM | |
Short update: to test what happens when commenting out the lines that delete temporary files, I commented them out.
Now the script runs well until the end; for the tailarach transformation, it says (this is run 08, others are similar):
#Script is running (command trimmed):
3dAllineate -base anat_avg+tlrc -1Dmatrix_apply sr906_frun08_bigal_tlrc_mat.aff12.1D -prefix sr906_frun08_tlrc_bigal+tlrc -input __tt_sr906_frun08_tsh+orig -verb -master SOURCE
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Nov 5 2008) [32-bit]
++ Authored by: Emperor Zhark
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_sr906_frun08_tsh+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./__tt_sr906_frun08_tsh+orig.BRIK is 2.567502 degrees from plumb.
++ Loading datasets
++ ========== Applying transformation to 172 sub-bricks ==========
++ ========== sub-brick #0 ==========
++ using -1Dmatrix_apply
++ Computing output image
[...]
++ ========== sub-brick #171 ==========
++ using -1Dmatrix_apply
++ Computing output image
++ Output dataset ./sr906_frun08_tlrc_bigal+orig.BRIK
++ total CPU time = 15.6 sec
++ ###########################################################
#Script is running (command trimmed):
3drefit -deoblique sr906_frun08_tlrc_bigal+tlrc
++ 3drefit: AFNI version=AFNI_2008_07_18_1710 (Nov 5 2008) [32-bit]
++ Authored by: RW Cox
** ERROR: Can't open dataset sr906_frun08_tlrc_bigal+tlrc
++ 3drefit processed 0 datasets
So for some reason (?!) 3dAllineate is doing computations but does not give the output file the +tlrc suffix. I'm really lost now
and any help is appreciated
Now the script runs well until the end; for the tailarach transformation, it says (this is run 08, others are similar):
#Script is running (command trimmed):
3dAllineate -base anat_avg+tlrc -1Dmatrix_apply sr906_frun08_bigal_tlrc_mat.aff12.1D -prefix sr906_frun08_tlrc_bigal+tlrc -input __tt_sr906_frun08_tsh+orig -verb -master SOURCE
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Nov 5 2008) [32-bit]
++ Authored by: Emperor Zhark
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_sr906_frun08_tsh+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./__tt_sr906_frun08_tsh+orig.BRIK is 2.567502 degrees from plumb.
++ Loading datasets
++ ========== Applying transformation to 172 sub-bricks ==========
++ ========== sub-brick #0 ==========
++ using -1Dmatrix_apply
++ Computing output image
[...]
++ ========== sub-brick #171 ==========
++ using -1Dmatrix_apply
++ Computing output image
++ Output dataset ./sr906_frun08_tlrc_bigal+orig.BRIK
++ total CPU time = 15.6 sec
++ ###########################################################
#Script is running (command trimmed):
3drefit -deoblique sr906_frun08_tlrc_bigal+tlrc
++ 3drefit: AFNI version=AFNI_2008_07_18_1710 (Nov 5 2008) [32-bit]
++ Authored by: RW Cox
** ERROR: Can't open dataset sr906_frun08_tlrc_bigal+tlrc
++ 3drefit processed 0 datasets
So for some reason (?!) 3dAllineate is doing computations but does not give the output file the +tlrc suffix. I'm really lost now
and any help is appreciated
| Subject | Author | Posted |
|---|---|---|
|
Nick Oosterhof | November 06, 2008 12:30PM |
|
Nick Oosterhof | November 06, 2008 02:17PM |
|
Daniel Glen | November 06, 2008 02:52PM |
|
Daniel Glen | November 07, 2008 11:44AM |
