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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:
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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 07, 2005 04:01PM | |
I usually do the following steps:
1-align anatomy to a "base" anatomy
2-use 3drotate -rotparent to repeat the rotation on the mask and statistical data.
We've noticed that the results are wrong in this case with the dataset below - but 3drotate -dfile and 3drotate -rotate .... -ashift ... (where I cut and paste the values) works fine.
Here are the steps (some details have been omitted, but can be seen in the 3dinfo output below):
%> 3dvolreg -base ../foo/bar+orig -dfile anat.reg.txt -prefix anat.reg anat+orig
%> 3dZeropad -z 2 -prefix mask.zpad mask+orig
%> 3drotate -rotparent anat.reg+orig -prefix mask.zpad.rotparent mask.zpad+orig
%> 3drotate -dfile anat.reg.txt -prefix mask.zpad.dfile mask.zpad+orig
I can upload some data if you want. I haven't checked to see if there are any other datasets showing similar problems.
3dinfo output:
%> 3dinfo anat.reg+orig
Dataset File: anat.reg+orig
Identifier Code: XYZ_RO-AmrMJuvWdOlOpxt6q6Q Creation Date: Mon Nov 7 14:26:28 2005
Dataset Type: Other MRI (-omri)
Byte Order: MSB_FIRST [this CPU native = MSB_FIRST]
Storage Mode: BRIK file
Data Axes Orientation:
first (x) = Inferior-to-Superior
second (y) = Left-to-Right
third (z) = Posterior-to-Anterior [-orient ILP]
R-to-L extent: -19.922 [R] -to- 19.922 [L] -step- 0.156 mm [256 voxels]
A-to-P extent: -12.000 [A] -to- 12.000 [P] -step- 1.500 mm [ 17 voxels]
I-to-S extent: -19.922 -to- 19.922 [S] -step- 0.156 mm [256 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is short: -1178 to 32502
----- HISTORY -----
[skoubpd@mr5: Fri Sep 9 13:49:51 2005] to3d -omri -prefix rn_8045c3 -session /da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid -view orig -xFOV 20.0000I-S -yFOV 20.0000L-R -zSLAB 18.0000P-0A -skip_outliers 3D:0:0:256:256:13:/da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid/rn_8045c3.temp
[skoubpd@mr5: Fri Sep 9 13:49:52 2005] 3drefit -zorigin 9.00000 /da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid/rn_8045c3+orig.HEAD
[skoubpd@mr5: Wed Oct 26 18:07:08 2005] 3dZeropad -z 2 -prefix rn_8045c3.zpad rn_8045c3+orig
[skoubpd@mr5: Wed Oct 26 18:07:17 2005] 3dvolreg -verbose -verbose -twopass -twodup -heptic -noclip -base ../../analysis/average.anat+orig -prefix rn_8045c3.reg -dfile rn_8045c3.reg.txt rn_8045c3.zpad+orig
[skoubpd@mr5: Wed Oct 26 18:10:05 2005] 3dvolreg did: -heptic -noclip -rotate 0.2402I 0.1091R -4.5267A -ashift -1.1285S -0.2971L 0.0151P
[hradivp@mr7: Mon Nov 7 14:26:28 2005] 3dcopy ../rn_8045c3.fid/rn_8045c3.reg+orig. /homes/hradivp/rotproblem/anat.reg
%> 3dinfo mask+orig
Dataset File: mask+orig
Identifier Code: XYZ_zcKyi_8qiQo9CLq6CK9OoA Creation Date: Mon Nov 7 14:25:41 2005
Dataset Type: Intensity (-fim)
Byte Order: MSB_FIRST [this CPU native = MSB_FIRST]
Storage Mode: BRIK file
Data Axes Orientation:
first (x) = Inferior-to-Superior
second (y) = Left-to-Right
third (z) = Posterior-to-Anterior [-orient ILP]
R-to-L extent: -19.844 [R] -to- 19.844 [L] -step- 0.312 mm [128 voxels]
A-to-P extent: -9.000 [A] -to- 9.000 [P] -step- 1.500 mm [ 13 voxels]
I-to-S extent: -19.844 -to- 19.844 [S] -step- 0.312 mm [128 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is byte: 0 to 1
----- HISTORY -----
[skoubpd@mr5: Fri Sep 9 13:49:51 2005] to3d -omri -prefix rn_8045c3 -session /da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid -view orig -xFOV 20.0000I-S -yFOV 20.0000L-R -zSLAB 18.0000P-0A -skip_outliers 3D:0:0:256:256:13:/da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid/rn_8045c3.temp
[skoubpd@mr5: Fri Sep 9 13:49:52 2005] 3drefit -zorigin 9.00000 /da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid/rn_8045c3+orig.HEAD
[skoubpd@mr5: Fri Sep 16 13:01:26 2005] 3dAutomask rn_8045c3+orig
[skoubpd@mr5: Fri Sep 16 13:05:25 2005] Drawing plugin COPY: Fill->Zero Type->Func
[skoubpd@mr5: Fri Sep 16 14:29:07 2005] Drawing plugin COPY: Fill->Data
[skoubpd@mr5: Wed Oct 26 18:06:59 2005] 3dresample -master rn_8045c9+orig -inset ../rn_8045c3.fid/rn_8045c3.bmask+orig -prefix rn_8045c9.bmask
[hradivp@mr7: Mon Nov 7 14:25:41 2005] 3dcopy rn_8045c9.bmask+orig. /homes/hradivp/rotproblem/mask
1-align anatomy to a "base" anatomy
2-use 3drotate -rotparent to repeat the rotation on the mask and statistical data.
We've noticed that the results are wrong in this case with the dataset below - but 3drotate -dfile and 3drotate -rotate .... -ashift ... (where I cut and paste the values) works fine.
Here are the steps (some details have been omitted, but can be seen in the 3dinfo output below):
%> 3dvolreg -base ../foo/bar+orig -dfile anat.reg.txt -prefix anat.reg anat+orig
%> 3dZeropad -z 2 -prefix mask.zpad mask+orig
%> 3drotate -rotparent anat.reg+orig -prefix mask.zpad.rotparent mask.zpad+orig
%> 3drotate -dfile anat.reg.txt -prefix mask.zpad.dfile mask.zpad+orig
I can upload some data if you want. I haven't checked to see if there are any other datasets showing similar problems.
3dinfo output:
%> 3dinfo anat.reg+orig
Dataset File: anat.reg+orig
Identifier Code: XYZ_RO-AmrMJuvWdOlOpxt6q6Q Creation Date: Mon Nov 7 14:26:28 2005
Dataset Type: Other MRI (-omri)
Byte Order: MSB_FIRST [this CPU native = MSB_FIRST]
Storage Mode: BRIK file
Data Axes Orientation:
first (x) = Inferior-to-Superior
second (y) = Left-to-Right
third (z) = Posterior-to-Anterior [-orient ILP]
R-to-L extent: -19.922 [R] -to- 19.922 [L] -step- 0.156 mm [256 voxels]
A-to-P extent: -12.000 [A] -to- 12.000 [P] -step- 1.500 mm [ 17 voxels]
I-to-S extent: -19.922 -to- 19.922 [S] -step- 0.156 mm [256 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is short: -1178 to 32502
----- HISTORY -----
[skoubpd@mr5: Fri Sep 9 13:49:51 2005] to3d -omri -prefix rn_8045c3 -session /da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid -view orig -xFOV 20.0000I-S -yFOV 20.0000L-R -zSLAB 18.0000P-0A -skip_outliers 3D:0:0:256:256:13:/da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid/rn_8045c3.temp
[skoubpd@mr5: Fri Sep 9 13:49:52 2005] 3drefit -zorigin 9.00000 /da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid/rn_8045c3+orig.HEAD
[skoubpd@mr5: Wed Oct 26 18:07:08 2005] 3dZeropad -z 2 -prefix rn_8045c3.zpad rn_8045c3+orig
[skoubpd@mr5: Wed Oct 26 18:07:17 2005] 3dvolreg -verbose -verbose -twopass -twodup -heptic -noclip -base ../../analysis/average.anat+orig -prefix rn_8045c3.reg -dfile rn_8045c3.reg.txt rn_8045c3.zpad+orig
[skoubpd@mr5: Wed Oct 26 18:10:05 2005] 3dvolreg did: -heptic -noclip -rotate 0.2402I 0.1091R -4.5267A -ashift -1.1285S -0.2971L 0.0151P
[hradivp@mr7: Mon Nov 7 14:26:28 2005] 3dcopy ../rn_8045c3.fid/rn_8045c3.reg+orig. /homes/hradivp/rotproblem/anat.reg
%> 3dinfo mask+orig
Dataset File: mask+orig
Identifier Code: XYZ_zcKyi_8qiQo9CLq6CK9OoA Creation Date: Mon Nov 7 14:25:41 2005
Dataset Type: Intensity (-fim)
Byte Order: MSB_FIRST [this CPU native = MSB_FIRST]
Storage Mode: BRIK file
Data Axes Orientation:
first (x) = Inferior-to-Superior
second (y) = Left-to-Right
third (z) = Posterior-to-Anterior [-orient ILP]
R-to-L extent: -19.844 [R] -to- 19.844 [L] -step- 0.312 mm [128 voxels]
A-to-P extent: -9.000 [A] -to- 9.000 [P] -step- 1.500 mm [ 13 voxels]
I-to-S extent: -19.844 -to- 19.844 [S] -step- 0.312 mm [128 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is byte: 0 to 1
----- HISTORY -----
[skoubpd@mr5: Fri Sep 9 13:49:51 2005] to3d -omri -prefix rn_8045c3 -session /da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid -view orig -xFOV 20.0000I-S -yFOV 20.0000L-R -zSLAB 18.0000P-0A -skip_outliers 3D:0:0:256:256:13:/da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid/rn_8045c3.temp
[skoubpd@mr5: Fri Sep 9 13:49:52 2005] 3drefit -zorigin 9.00000 /da/mr/data/mr_data/rat_neuroscience_brain/study_030905/08-04-05/rn_8045c3.fid/rn_8045c3+orig.HEAD
[skoubpd@mr5: Fri Sep 16 13:01:26 2005] 3dAutomask rn_8045c3+orig
[skoubpd@mr5: Fri Sep 16 13:05:25 2005] Drawing plugin COPY: Fill->Zero Type->Func
[skoubpd@mr5: Fri Sep 16 14:29:07 2005] Drawing plugin COPY: Fill->Data
[skoubpd@mr5: Wed Oct 26 18:06:59 2005] 3dresample -master rn_8045c9+orig -inset ../rn_8045c3.fid/rn_8045c3.bmask+orig -prefix rn_8045c9.bmask
[hradivp@mr7: Mon Nov 7 14:25:41 2005] 3dcopy rn_8045c9.bmask+orig. /homes/hradivp/rotproblem/mask
| Subject | Author | Posted |
|---|---|---|
|
Vince | November 07, 2005 04:01PM |
|
Vince | November 09, 2005 01:40PM |
|
bob cox | November 09, 2005 02:28PM |
|
Godot | November 09, 2005 04:19PM |
|
Vince | November 09, 2005 06:05PM |
|
Godot | November 14, 2005 12:12AM |
|
Vince | November 14, 2005 11:09AM |
