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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
| August 11, 2009 12:25AM | |
Hi,
I noticed this bug several months ago but am just now getting around to reporting it after confirming it hasn't been fixed since then.
In composing the 3dREML command, 3dDeconvolve appears to append "_REML" to output filenames blindly, with the result only being appropriate if no suffixes and/or extensions were included in the output filenames. (In this case it doesn't discriminate between BRIK and NIfTI. :-p)
See the last three lines of this (edited) example REML_cmd:
3dREMLfit -matrix Decon+orig.xmat.1D \
-input "ra1008_01+orig.nii [...] ra1008_20+orig.nii" \
-mask masks/ra1008_01_automask+orig.nii.gz \
-Rbeta Decon_coefs+orig.BRIK.gz_REML -fout -tout -rout \
-Rbuck Decon+orig.BRIK.gz_REML -Rvar Decon+orig.BRIK.gz_REMLvar \
-Rerrts Decon_res+orig.nii.gz_REML -verb
...which I presume were meant to be:
-Rbeta Decon_coefs_REML+orig.BRIK.gz -fout -tout -rout \
-Rbuck Decon_REML+orig.BRIK.gz -Rvar Decon_REMLvar+orig.BRIK.gz \
-Rerrts Decon_res_REML+orig.nii.gz -verb
An unedited copy is attached of that REML_cmd with the original call to 3dDeconv is attached.
Thanks,
Terry
P.S. Nevermind, I guess I can't attach text. If you'd like to see it, let me know. Otherwise, I'll spare you the probably unnecessary text dump.
I noticed this bug several months ago but am just now getting around to reporting it after confirming it hasn't been fixed since then.
In composing the 3dREML command, 3dDeconvolve appears to append "_REML" to output filenames blindly, with the result only being appropriate if no suffixes and/or extensions were included in the output filenames. (In this case it doesn't discriminate between BRIK and NIfTI. :-p)
See the last three lines of this (edited) example REML_cmd:
3dREMLfit -matrix Decon+orig.xmat.1D \
-input "ra1008_01+orig.nii [...] ra1008_20+orig.nii" \
-mask masks/ra1008_01_automask+orig.nii.gz \
-Rbeta Decon_coefs+orig.BRIK.gz_REML -fout -tout -rout \
-Rbuck Decon+orig.BRIK.gz_REML -Rvar Decon+orig.BRIK.gz_REMLvar \
-Rerrts Decon_res+orig.nii.gz_REML -verb
...which I presume were meant to be:
-Rbeta Decon_coefs_REML+orig.BRIK.gz -fout -tout -rout \
-Rbuck Decon_REML+orig.BRIK.gz -Rvar Decon_REMLvar+orig.BRIK.gz \
-Rerrts Decon_res_REML+orig.nii.gz -verb
An unedited copy is attached of that REML_cmd with the original call to 3dDeconv is attached.
Thanks,
Terry
P.S. Nevermind, I guess I can't attach text. If you'd like to see it, let me know. Otherwise, I'll spare you the probably unnecessary text dump.
| Subject | Author | Posted |
|---|---|---|
|
Terry Nycum | August 11, 2009 12:25AM |
