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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:
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
History of AFNI updates
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Hi Daniel,
Does it make sense to perform volreg on DWI datasets? Each volume represents a spearate gradient and hence a different contrast. So, is there a cost function that can align volumes with differing contrasts gradient-to-gradient?
Thank you
by
_durai_
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AFNI Message Board
Hi Rick, blur and regress blocks complain when I remove the mask block.
-- tcat: reps is now 152
-- volreg: base/sub indices are 0, 0
++ volreg: warping to isotropic 3 mm tlrc voxels
++ updating polort to 3, from run len 380.0 s
-- empty file /home/owner/task1/rontask_Data/RON3/data/PSK403/timing/NoResponse.txt okay as local_times
** empty stim file /home/owner/task1/rontask_Data/RON3/dat
by
_durai_
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AFNI Message Board
Thanks Rick, indeed it was based on example 8. Here is the command used to generate the script:
# afni_proc.py -subj_id 403 -script afni_psk_403.tcsh -out_dir \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/403.proced -blocks \
# tshift align tlrc volreg surf blur mask scale regress -dsets \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/PS
by
_durai_
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AFNI Message Board
And fyi, here is the 3dVol2Surf command that was used to create the niml dset (which was then blurred using SurfSmooth):
# map volume data to the surface of each hemisphere
foreach hemi ( lh rh )
foreach run ( $runs )
3dVol2Surf -spec $surface_dir/PSK403_${hemi}.spec \
-sv ${subj}_SurfVol_Alnd_Exp+tlrc \
-surf_A sm
by
_durai_
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AFNI Message Board
Hi Afni experts,
I was running the surface version of afni_proc and at the mask creation block :
# create 'full_mask' dataset (union mask)
foreach run ( $runs )
3dAutomask -dilate 1 -prefix rm.mask_r$run \
pb04.$subj.$hemi.r$run.blur.niml.dset
end
I encountered the following error :
++ 3dAutomask: AFNI version=AFNI_2011_12_21_1014 (
by
_durai_
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AFNI Message Board
Hi AFNI experts,
This is an example usage of the command from the SUMA documentation. I am having difficulty understanding why the spec file is in standard space but the smoothwm and pial are in subject space, as the spec file specifies the relationship between surfaces used?
3dVol2Surf
-spec ../SurfData/SUMA/std.DemoSubj_lh.spec \
-surf_A lh.smoothwm.asc \
-surf_B lh.pial.asc \
-sv Dem
by
_durai_
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AFNI Message Board
To clarify further, consider two parallel runs of align_epi_anat with different deoblique options. The result is always plumb.
align_epi_anat -deoblique off -anat T1 -epi b0........ -> Plumb_T1_al + inv_mat_1
align_epi_anat -deoblique on -anat T1 -epi b0..........-> Plumb_T1_al + inv_mat_2
Is inv_mat_1 = inv_mat_2??
If not, when I attempt a reverse alignment using 3dallineate,
by
_durai_
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AFNI Message Board
Dear AFNI experts,
I used align_epi_anat.py to align a T1 to a b0 image. Now I get 2 mat files - T1_al_mat_aff12.1D and T1_al_e2a_only_mat.aff12.1D.
My first question is, is the second one the inverse matrix?
I tried to find this out by supplying it to 3dallineate and aligning the b0 to the T1(inverse of what was done before). However the result is confusing because of obliquity.
So m
by
_durai_
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AFNI Message Board
update : the obliqued dataset looks oblique in the viewer but I wonder why it says Plumb in the header.......?
by
_durai_
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AFNI Message Board
Hi AFNI experts,
So I tried to oblique my T1 to my DWI. The output goes to Plumb instead for some reason that is not obvious to me. Thanks for your help!
3dWarp -card2oblique ./d60_1/afni_nodif_brain+orig. -prefix afni_obq_mp_ns_t3d afni_mp_ns_t3d+orig.
owner@> 3dinfo ./d60_1/afni_nodif_brain+orig. | grep Axes
++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (Jan 31 2014) [64-bit]
Data
by
_durai_
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AFNI Message Board
Hi AFNI experts,
I tried using align_epi_anat to align my skull stripped T1 to DWI b0 image. I have used this command in the past to align two non-time series datasets with just 1 subbrik each. But this time it throws a 3dTstat error....
align_epi_anat -dset1 dwi.nii.gz -dset2 T1_noskull.nii -dset2to1 -dset1_strip None -dset2_strip None -suffix _mp2diff -AddEdge
#++ align_epi_anat versio
by
_durai_
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AFNI Message Board
Thanks Ziad, the GIFTI option still gives stuff in non-native space. And the SUMA-GIFTI space is different from both the native and the regular SUMA space.. Using FS commands for now..seems to work.
by
_durai_
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AFNI Message Board
Hi AFNI experts,
After you do SUMA_Make_Spec_FS on FS segmentations what grid do they go into? I haven't checked well but it is not native space for sure. What is a good way to get the rois,surfaces in the SUMA folder to native space?
Thank you
by
_durai_
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AFNI Message Board
Hi Daniel, I tried what you suggested and also removed -giant_move. And here are the before and after pictures:
before
after
It is very good. Do you think alignment could be improved further?
by
_durai_
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AFNI Message Board
Daniel, thanks. That did work. However it resulted in a much worse "alignment" than the original datasets. Any idea why? Below is a url to the picture. Something is obviously very wrong with the command..
T1orig-T2orig-T2align
by
_durai_
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AFNI Message Board
Hi afni experts,
I am trying to register a T2W partial structural image to a whole brain T1 MPRAGE. Both are skull stripped and the T2W was resampled to the same dimensions as the T1 prior to using the following command. I used this command as I read that align_api_anat can do intramodality alignment as well.
align_epi_anat.py -dset1 t5_MP_ns.nii -dset2 t5_tse_ns_rsmp.nii -dset2to1 -cost nm
by
_durai_
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AFNI Message Board