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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
| January 02, 2019 02:52PM | |
Hi, Daniel
Thanks for your reply!. I did try to avoid the skull-stripping step. I cleaned up my cmd a little bit. As you can see, I set '-dset1_strp None -dset2_strip None'
align_epi_anat.py -dset1 dset.nii.gz -dset2 dset2.nii.gz -master_dset2 dset2.nii.gz -suffix _al.nii.gz -dset1to2 -output_dir outputdir -giant_move -dset1_strip None -dset2_strip None -overwrite -rigid_body -Allineate_opts -weight dset2_brainmask.nii.gz
But it still internally add a -weight input. Did I miss something?
#Script is running (command trimmed):
3dAllineate -lpa -wtprefix ./__tt_dset2.nii.gz_wtal -weight ./__tt_dset1_ts_wt+orig -source ./__tt_dset2 -prefix ./dset1.nii.gz -base ./__tt_dset2_ts+orig -cmass -1Dmatrix_save ./dset2_al.nii.gz_mat.aff12.1D -master BASE -mast_dxyz 0.500000 -weight ./dset1_brainmask.nii.gz -twobest 11 -twopass -VERB -maxrot 45 -maxshf 40 -fineblur 1
-source_automask+2
++ 3dAllineate: AFNI version=AFNI_18.2.19 (Sep 27 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: Small value 0.5 after -mast_dxyz
** FATAL ERROR: Can't have multiple -weight options
** Program compile date = Sep 27 2018
** 3dAllineate failure
** ERROR - script failed
thanks.
ruyuan
Thanks for your reply!. I did try to avoid the skull-stripping step. I cleaned up my cmd a little bit. As you can see, I set '-dset1_strp None -dset2_strip None'
align_epi_anat.py -dset1 dset.nii.gz -dset2 dset2.nii.gz -master_dset2 dset2.nii.gz -suffix _al.nii.gz -dset1to2 -output_dir outputdir -giant_move -dset1_strip None -dset2_strip None -overwrite -rigid_body -Allineate_opts -weight dset2_brainmask.nii.gz
But it still internally add a -weight input. Did I miss something?
#Script is running (command trimmed):
3dAllineate -lpa -wtprefix ./__tt_dset2.nii.gz_wtal -weight ./__tt_dset1_ts_wt+orig -source ./__tt_dset2 -prefix ./dset1.nii.gz -base ./__tt_dset2_ts+orig -cmass -1Dmatrix_save ./dset2_al.nii.gz_mat.aff12.1D -master BASE -mast_dxyz 0.500000 -weight ./dset1_brainmask.nii.gz -twobest 11 -twopass -VERB -maxrot 45 -maxshf 40 -fineblur 1
-source_automask+2
++ 3dAllineate: AFNI version=AFNI_18.2.19 (Sep 27 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: Small value 0.5 after -mast_dxyz
** FATAL ERROR: Can't have multiple -weight options
** Program compile date = Sep 27 2018
** 3dAllineate failure
** ERROR - script failed
thanks.
ruyuan
| Subject | Author | Posted |
|---|---|---|
|
ruyuanzhang | December 30, 2018 11:39PM |
|
Daniel Glen | December 31, 2018 12:27PM |
|
ruyuanzhang | January 02, 2019 02:52PM |
|
Daniel Glen | January 02, 2019 03:47PM |
|
ruyuanzhang | January 10, 2019 05:24PM |
|
Daniel Glen | January 10, 2019 05:29PM |
|
ruyuanzhang | January 11, 2019 12:58AM |
