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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
| February 09, 2018 11:13AM | |
Hi all,
I am working on using @toMNI_Qwarpar to create a nonlinearly warped atlas for my dataset. I have run @toMNI_Awarp successfully on each individual dataset, and am trying to run @toMNI_Qwarpar in the directory created by @toMNI_Awarp.
However, when I run @toMNI_Qwarpar I receive this fatal error message and the script eventually dies:
[williamss@node10 OASESatlas_2009]$ ./OASES_qwarp.sh
========== @toMNI_Qwarp: Compute A level mean (affine) ==========
++ 3dMean: AFNI version=AFNI_17.0.18 (Mar 29 2017) [64-bit]
========== @toMNI_Qwarp: Compute B level (minimum patch = 101) ==========
=== Processing 48 datasets in 8 jobs
=== Bottom index list = 1 7 13 19 25 31 37 43
=== Top index list = 6 12 18 24 30 36 42 48
[1] 22559
205_MPRAGE_strip_uni+tlrc.HEAD 206_MPRAGE_strip_uni+tlrc.HEAD 207_MPRAGE_strip_uni+tlrc.HEAD 217_MPRAGE_strip_uni+tlrc.HEAD 222_MPRAGE_strip_uni+tlrc.HEAD 224_MPRAGE_strip_uni+tlrc.HEAD
++ OpenMP thread count = 1
++ 3dQwarp: AFNI version=AFNI_17.0.18 (Mar 29 2017) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
** FATAL ERROR: base-source dataset grid mismatch
: try the -resample option
This goes on and pops up for each file in the dataset.
I tried running:
3dinfo -same_grid DSET1 DSET2 and 3dinfo -orient -d3 -nijk -o3 -space -prefix DSET1 DSET2 to compare my individual volumes to the base template I'm using, per suggestions I found in other message boards, and I get the following outcomes:
[williamss@login01 OASESatlas_2009]$ 3dinfo -same_grid MNI152_T1_2009c+tlrc.HEAD 206_MPRAGE_strip_uni+tlrc.HEAD
1
1
[williamss@login01 OASESatlas_2009]$ 3dinfo -orient -d3 -nijk -o3 -space -prefix MNI152_T1_2009c+tlrc.HEAD 206_MPRAGE_strip_uni+tlrc.HEAD
LPI -1.000000 -1.000000 1.000000 8530021 96.000000 132.000000 -78.000000 MNI MNI152_T1_2009c
LPI -1.000000 -1.000000 1.000000 8530021 96.000000 132.000000 -78.000000 MNI 206_MPRAGE_strip_uni
These outcomes are similar for my other volumes as well, so it seems they are all on the same grid, as they should be.
I also tried adding -resample to 3dQwarp in the B level warp and still received the same error.
The version of AFNI currently being used is Mar 29 2017 (Version AFNI_17.0.18) as I'm working off a high performance cluster. If anyone thinks it would help I can see if a newer version can be added.
Thanks in advance. Any help you can provide would be appreciated!
Best,
Sam Williams
Edited 1 time(s). Last edit at 02/11/2018 10:55AM by sewilliams.
I am working on using @toMNI_Qwarpar to create a nonlinearly warped atlas for my dataset. I have run @toMNI_Awarp successfully on each individual dataset, and am trying to run @toMNI_Qwarpar in the directory created by @toMNI_Awarp.
However, when I run @toMNI_Qwarpar I receive this fatal error message and the script eventually dies:
[williamss@node10 OASESatlas_2009]$ ./OASES_qwarp.sh
========== @toMNI_Qwarp: Compute A level mean (affine) ==========
++ 3dMean: AFNI version=AFNI_17.0.18 (Mar 29 2017) [64-bit]
========== @toMNI_Qwarp: Compute B level (minimum patch = 101) ==========
=== Processing 48 datasets in 8 jobs
=== Bottom index list = 1 7 13 19 25 31 37 43
=== Top index list = 6 12 18 24 30 36 42 48
[1] 22559
205_MPRAGE_strip_uni+tlrc.HEAD 206_MPRAGE_strip_uni+tlrc.HEAD 207_MPRAGE_strip_uni+tlrc.HEAD 217_MPRAGE_strip_uni+tlrc.HEAD 222_MPRAGE_strip_uni+tlrc.HEAD 224_MPRAGE_strip_uni+tlrc.HEAD
++ OpenMP thread count = 1
++ 3dQwarp: AFNI version=AFNI_17.0.18 (Mar 29 2017) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
** FATAL ERROR: base-source dataset grid mismatch
: try the -resample option
This goes on and pops up for each file in the dataset.
I tried running:
3dinfo -same_grid DSET1 DSET2 and 3dinfo -orient -d3 -nijk -o3 -space -prefix DSET1 DSET2 to compare my individual volumes to the base template I'm using, per suggestions I found in other message boards, and I get the following outcomes:
[williamss@login01 OASESatlas_2009]$ 3dinfo -same_grid MNI152_T1_2009c+tlrc.HEAD 206_MPRAGE_strip_uni+tlrc.HEAD
1
1
[williamss@login01 OASESatlas_2009]$ 3dinfo -orient -d3 -nijk -o3 -space -prefix MNI152_T1_2009c+tlrc.HEAD 206_MPRAGE_strip_uni+tlrc.HEAD
LPI -1.000000 -1.000000 1.000000 8530021 96.000000 132.000000 -78.000000 MNI MNI152_T1_2009c
LPI -1.000000 -1.000000 1.000000 8530021 96.000000 132.000000 -78.000000 MNI 206_MPRAGE_strip_uni
These outcomes are similar for my other volumes as well, so it seems they are all on the same grid, as they should be.
I also tried adding -resample to 3dQwarp in the B level warp and still received the same error.
The version of AFNI currently being used is Mar 29 2017 (Version AFNI_17.0.18) as I'm working off a high performance cluster. If anyone thinks it would help I can see if a newer version can be added.
Thanks in advance. Any help you can provide would be appreciated!
Best,
Sam Williams
Edited 1 time(s). Last edit at 02/11/2018 10:55AM by sewilliams.
| Subject | Author | Posted |
|---|---|---|
|
sewilliams | February 09, 2018 11:13AM |
