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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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Pages: 12
Results 1 - 30 of 39
Dear AFNI experts,
I'm trying to use SurfMesh to generate higher density meshes with something like:
SurfMesh -i SUMA/lh.smoothwm.gii -o SUMA.hd/lh.smoothwm.gii -edges 2
SurfMesh -i SUMA/lh.pial.gii -o SUMA.hd/lh.pial.gii -edges 2
The meshes are generated without error and the number of faces doubled as expected.
However, the order of vertices seems to be randomized, so that the co
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herrlich10
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AFNI Message Board
One rationale backing the current approach might be that we first need to regress out the (possibly existing) signals imposed by the driving input in order to generate data composed of pure noise. Is my understanding correct?
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herrlich10
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AFNI Message Board
Dear AFNI gurus,
I'm trying to understand the permutation tests provided by 3dttest++, especially the ETAC method which is truly an ingenious solution to the cluster defining p trade-off problem. I have a question though, regarding the construction of the permuted, pure-noise dataset.
In the simplest permutation tests (comparing two-sample or one-sample mean), we permute or sign-flip the
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herrlich10
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AFNI Message Board
Thank you for your answers! Even knowing sth cannot be done make me feel more comfortable than keep puzzling:P
I'll check those tutorial videos. Very grateful for your effort to make them freely available on youtube.
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herrlich10
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AFNI Message Board
Dear Danial and Paul,
Thank you very much for pointing out the LabelDset field in the *.spec file, which is exactly what I want.
With some trial-and-errors, I was able to display HCP-MMP1 (https://figshare.com/articles/dataset/HCP-MMP1_0_projected_on_fsaverage/3498446) annotation in SUMA. In case someone search for this in the future, I read out the color table from the lh.HCP-MMP1.annot, ma
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herrlich10
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AFNI Message Board
Dear AFNI/SUMA experts,
SUMA seems to use a default annotation dset (aparc.a2009s.annot), so that an anatomical label is displayed for each surface vertex, both in the main window and in Xhair Info panel of Surface Controller.
I would like to use another annotation dset for this purpose. (Q1) How can I change which dset to use? (apart from replacing aparc.a2009s.annot.niml.dset with my own
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herrlich10
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AFNI Message Board
Hi afni experts,
When I'm trying to convert a functional dataset with only one slice from DICOM files with something like:
to3d -prefix test.nii -time:zt 1 120 3000 alt+z2 *.IMA
The program complains about:
*+ WARNING: Bad DICOM header - assuming oblique scaling direction!
++ Command line TR=3000ms ; Images TR=3s
++ Making widgets.....
Then enters into interactive mo
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herrlich10
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AFNI Message Board
Dear afni experts,
I would like to know how does 3dDeconvolve -gltsym compute the t statistics for simple contrasts.
I thought I should be able to get the same results manually.
For a simple study having two conditions, A and B, I'd like to compute the t-stat for +A -B.
I used the following formula:
C =
X is design matrix from X.test.xmat.1D
dof (degrees of freedom) can be found
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herrlich10
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AFNI Message Board
Hi afni experts,
I have a pair of T1 and EPI which I manually coregistered (for some reason) in FreeSurfer, using the following command:
tkregister2 --s subj_id --mov epi.nii --surf orig --reg register.dat --regheader
Now with the affine transform matrix at hand (in the register.dat file), I would like to apply it to the T1 volume in AFNI, using 3dAllineate.
However, due to the incompat
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herrlich10
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AFNI Message Board
1) Difference between native mesh and standard mesh
I open the meshes with the following commands, and press Z for the same number of times to arrive at presumably the same view point:
suma -i lh.smoothwm.asc &
suma -i std.200.lh.smoothwm.asc &
As shown in the attached picture, the difference are mainly two-fold:
First, there seems to be a small global shift in the std mesh (leftward
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herrlich10
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AFNI Message Board
Thank you Daniel~ Nice to hear from you.
I've tried MapIcosahedron via @SUMA_Make_Spec_FS approach, but it only affects the std.ld.* surfaces (i.e., standard meshes), but not the native meshes (i.e., ?h.*.asc). This is understandable since the -ld parameter is used during the creation of the new icosahedron mesh which is mapped to the sphere.reg mesh.
Is it possible to upsample the nativ
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herrlich10
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AFNI Message Board
Dear afni experts,
I would like to upsample suma surface meshes (so that each of them comprises more vertices and faces) to potentially achieve better accuracy when projecting back and forth between volumetric and surface representations.
SurfMesh seems to the function for this purpose. However, each execution of the following command
SurfMesh -edges 2 -i_fs lh.smoothwm.asc -o_fs hd.lh.s
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herrlich10
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AFNI Message Board
Hi afni experts,
Here is a follow up question: without using 3dSurfMask, which doesn't support volume masking and is very slow,
1) Is it possible to get signed distance from a surface for a list of voxels?
2) Alternative, is it possible to determine whether a list of voxels are inside or outside a closed surface (which apparently could be concave)?
I realize that this is the true com
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herrlich10
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AFNI Message Board
Thanks, Daniel~
But if I have a single *.niml.dset that contains vertices and associated surface data for both hemispheres, how can I load and visualize it in SUMA?
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herrlich10
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AFNI Message Board
Dear afni experts,
I'm using AFNI/FreeSurfer/SUMA tool chain, and CoSMoMVPA matlab package to do surface-based MVPA, and encountered a few problems. Any help would be highly appreciated.
1) According to the CoSMoMVPA demo, its surface-based searchlight routine seems to require merged hemisphere (mh, as opposed to lh+rh) format of the FS surface (in *.asc file). However, @SUMA_Make_Spec
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herrlich10
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AFNI Message Board
Wow, I'll try this new approach.
Thank you very much, Daniel~
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herrlich10
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AFNI Message Board
Dear AFNI experts,
I use 3dSurfMask to compute distance between voxels and specified surface. Since it is quite time consuming (no OpenMP), esp. for high resolution grid_parent, is it possible to restrict the computation within a mask?
Many thanks~
Best regards,
Chencan
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herrlich10
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AFNI Message Board
Dear AFNI experts,
In some of the fMRI runs, the cardiac (pulse) sensor malfunctioned and the cardiac data were either corrupted or flat (the value holds constant over time, which will cause PeakFinder.py to return [] and crash the program).
Is it possible to use RetroTS.py with only the remaining respiration data?
BTW, which one works better, RetroTS.py or 3dretroicor?
Thanks a lot!
B
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herrlich10
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AFNI Message Board
Dear AFNI team,
Recently, I realize that using AFNI by writing ipython script (*.ipy) is highly enjoyable compared with tcsh or bash scripts,
except for the Python 2/3 compatibility issue.
Although Python 2 and 3 have been running in parallel for a long time, but currently I feel the migrating speed toward Python 3 is accelerating.
For example,
1) Python 2.7 stops to get feature back p
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herrlich10
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AFNI Message Board
Hi, everyone~
I have exactly the same problem: 0.7 mm iso T1, freesurfer surfaces are OK, but SurfVol+orig is only 1x1x1 by @SUMA_Make_Spec_FS -sid $subj.
1) Is it a problem?
2) Shall I 3dresample SurfVol+orig to 0.7 mm?
3) Is there a way to get 0.7 mm SurfVol+orig natively out of @SUMA_Make_Spec_FS?
Thanks a lot!
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herrlich10
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AFNI Message Board
Thank you very much! All the pieces now fit to each other:D
Just as a quiz to myself,
FT_anat_ns+tlrc::WARP_DATA must be a matrix that maps points in standard space back to native space. Right?:)
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herrlich10
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AFNI Message Board
Many thanks ptaylor~ Nicely explained.
I've read this mechanism in the help for 3dNwarpApply, but I didn't realize that it also applies to cat_matvec.
An important question arises though: when to use -I to take the inversion?
If I align_epi_anat.py dset1 to dset2, which gives me a dset1_mat.aff12.1D,
and align_epi_anat.py dset2 to dset3, which gives me a dset2_mat.aff12.1D.
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herrlich10
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AFNI Message Board
Hi everyone,
I'm sorry but I'm getting a little confused about cat_matvec.
I defined two 3x3 matrices A and B, and did
cat_matvec A B > C
and fould C=B*A, which suggests transform A is applied first, and then B is applied.
This is exactly what the doc describes.
So if I'd like to volreg a dset, then align it to anat, I should do
cat_matvec volreg align > combined
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herrlich10
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AFNI Message Board
Hi rick:)
Since I also need blip, align, etc. which are shared by all 12 runs, so a single preprocess batch until regression would be great.
I don't really understand what do you mean by "done in a single regression". If you're suggesting to use an omnibus design matrix like the following:
My main concern is that, would it be a waste of degrees of freedom to include i
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herrlich10
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AFNI Message Board
Thanks rick~
Actually, I use Dimon to read dicom files, though I know Dicom uses to3d internally to do the job.
Now I understand that the slice timing info must be either:
1) inferred somehow by Dimon and passed to to3d as tpattern
or
2) inferred by to3d itself if FROM_IMAGE is given as tpattern
Could you explain how does Dimon or to3d infer the tpattern from raw dicom files? Is it some
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herrlich10
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AFNI Message Board
Dear experts,
For an EPI dataset, there is slice timing information in the .HEAD file. However, I couldn't find similar information in the header read by dicom_hdr from the raw dicom file (in case it is relevant, I have only one *.IMA file per volume).
So how does to3d determine the slice order (i.e., based on which item in the dicom header)? Is this information reliable if given?
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herrlich10
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AFNI Message Board
Dear experts,
For an experiment containing 12 runs and 3 tasks (A, B, C) arranged in an interleaved manner (A-B-C-A-B-C-A-B-C-A-B-C), is it possible to construct a single afni_proc.py command to preprocess all 12 runs together (so that, e.g., we may have a better quality mean EPI volume) and do 3 separate 3dDeconvolve for each of the tasks?
If not, is it possible to use afni_proc.py in two
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herrlich10
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AFNI Message Board
Reinstalled anaconda (Python 3.5.2 |Anaconda 4.2.0 (x86_64)), now OpenMP works in jupyter notebook.
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herrlich10
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AFNI Message Board
Thanks, rick! This is really cool!
In case someone else is also interested in similar functionality, here is my current approach:
After opening multiple afni controllers, I save my multi-controller layout (as well as underlay, overlay, color, threshold, etc. associated with each controller) by:
Define Datamode > Misc > Save Layout > layout01.script (N.B.: file name must contain &quo
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herrlich10
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AFNI Message Board
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