Show all posts by user
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
Results 2221 - 2250 of 2305
Hi-
50 is indeed there because it is a short number. I think the FSL number of 5000 might relate to their number of iterations for tracking (and a similar number is warranted when using AFNI and '3dTrackID -mode PROB'... but that's another story.)
I generally use something around 250-300. I'm working on the more scientific rationale for numbers around that size, but ba
by
ptaylor
-
AFNI Message Board
Makes sense, thanks.
Perhaps an example like this should be added to either/both the 3dNwarpApply and auto_warp.py help files?
--pt
by
ptaylor
-
AFNI Message Board
Hi-
I'm using auto_warp.py to map a data set from native DWI space to standard TT space. I then want to apply the same warp to a set of ROIs I've been using in native DWI space.
I am using 3dNwarpApply to apply the transform to the ROIs. However, I can't manage to get the final result in the right space. Which of the outputs of auto_warp.py do I apply? I have tried even
by
ptaylor
-
AFNI Message Board
I believe that, by default, 3dFourier uses linear detrending, whereas 3dBandpass uses quadratic detrending. (Though other internal differences may exist, on which others can comment.)
If you are using 3dBandpass for RS-FMRI analysis, you could use 3dRSFC instead, which has 3dBandpass internally at its heart but adds the functionality of calculating RSFC parameters (ALFF, fALFF, RSFA, etc.) at
by
ptaylor
-
AFNI Message Board
The AFNI-FATCAT (Taylor & Saad, 2013) set of programs has been updated to v2.1.
In the process of updating from FATCAT v1.1, several small and a few large features have changed, including:
the inclusion of multi-directional tracking for HARDI-modeled data (3dTrackID); improvements in SUMA-visualization capability (so one should make sure to have an uptodate version of SUMA, as well);
by
ptaylor
-
AFNI Message Board
Ok, just to log the resolution of all this: my understanding was incorrect of the usage of 3dNwarpApply was incorrect. With the following nonlinear warp from T1 -> DWI made:
3dQwarp -duplo -allineate -pear \
-prefix T1_in_DWI_Q \
-base mean_dwi.nii.gz \
-source T1.nii.gz \
-overwrite
Then the following application of 3dNwarpApply with just the *WARP* file gui
by
ptaylor
-
AFNI Message Board
Hi-
And, relating this post to a recent one about the addition of the 1dDW_Grad_o_Mat program, it should be noted that the order of 3dDWItoDT's matrix elements (=columns in either the '-bmatrix_Z' or '-bmatrix_NZ' FILE) is the 'diagonal' first format, such as:
B_xx B_yy B_zz B_xy B_xz B_yz.
In the 1dDW_Grad_o_Mat naming, this is the 'AFNI'-
by
ptaylor
-
AFNI Message Board
Hmm, using just '-resample' instead of 'allineate' gave me a partial brain output set (it's over the edge of the window); but then at least applying the warp with 3dNwarpApply gave the same (albeit partial) output...
--pt
by
ptaylor
-
AFNI Message Board
Ah, right, that makes more sense...
They are, yes; they have the same orientation, origin and voxel size. But also, since application to the anat again itself doesn't work...
-pt
by
ptaylor
-
AFNI Message Board
If the sets are on different grids (as they are here), then it seems like either -allineate or -resample is necessary. When I took away -allineate, then I get a:
** FATAL ERROR: base-source dataset grid mismatch : try the -resample option
I'm trying with -resample instead now.
In the past, I think I've been fine using the -allineate and using 3dNwarpApply as first described.
by
ptaylor
-
AFNI Message Board
They are both RPI.
The anatomical is 1x1x1, and the DWI is 1.6x1.6x4 (not by my choice...). But I don't see how that would affect things badly, since the transform worked ok in Qwarp.
--pt
by
ptaylor
-
AFNI Message Board
That gives almost exactly the same result (to ~3 decimals) as the:
-nwarp 'T1_in_DWI_Q_WARP+orig T1_in_DWI_Q_Allin.aff12.1D'
--pt
by
ptaylor
-
AFNI Message Board
Hi-
There's a new program in the latest source codes (Jan. 8 and after-- NB, it exists with a bug in the Dec. 27 build) to help deal with manipulating DWI gradient/*.bvec/bmatrix files. There's lots of formats for these things variously output by programs which convert dicom->nifti, and also lots of inputs for various programs to use them:
+ rows vs columns;
+ having b=0 rows
by
ptaylor
-
AFNI Message Board
Hi-
I'm trying to 1) align an anatomical to a mean DWI image, and the 2) apply the resulting warp to an ROI which is defined in the anatomical space.
I use the following to make the transformation from A(natomical) -> mean_DWI:
$ 3dQwarp -duplo -allineate -pear \
-prefix T1_in_DWI_Q \
-base mean_DWI.nii.gz \
-source A.nii.gz \
-overwrite
and the results loo
by
ptaylor
-
AFNI Message Board
Hi-
The problem lies in: Nseed_X="0"
There can't be any zeros in the 'number of seeds' along a given direction.
Usually, I would assume that the Nseeds_* would be probably the same:
For 1 seed in the center of a voxel:
Nseed_X="1"
Nseed_Y="1"
Nseed_Z="1"
For having 8, equally/isotropically spaced seeds in each voxel:
Nsee
by
ptaylor
-
AFNI Message Board
Hi,
I think I'm doing something wrong using whereami and also with loading atlases.
When I right-click on an AFNI viewer window for `whereami'ing, I get a lot of messages of reading different atlases and my memory usage goes to max (Mac OS 10.6.8, 4GB RAM), with my computer ~freezing, and I have to force quit the process.
Additionally, when I try to click on one of the TT_desai
by
ptaylor
-
AFNI Message Board
Hi,
In how I originally wrote this program, I checked some inputs as they were read in, which was a bit silly because it required the commandline options to be 'ordered' (I hadn't noticed as I was debugging as I kept using variations of the same order). I suspect this might be the problem (which will soon be resolved...).
Therefore, please try:
$ 3dProbTrackID -det_net AND
by
ptaylor
-
AFNI Message Board
They are viewable as AFNI volumes, and making a montage is usually useful, for one.
One thing I've done in the past, using TrackVis, is to:
+ take a single brik of WM connections.
+ turn it into a binary mask ( e.g., --> $ 3dcalc -a FILE -expr 'step(a)' -prefix MASK_OUT.nii.gz )
+ load it into TrackVis as an ROI ( ROI -> New ROI from Nifti/Analyze Image...).
That is
by
ptaylor
-
AFNI Message Board
Hi (and happy New Year)-
A couple things:
Currently, '3dTrackID -logic {AND | OR}' has been superceded by '3dProbTrackID -det_net {AND | OR}'. Basically, deterministic and probabilistic tracking were originally two different programs, but I merged them for consistency/ease of updating. The naming is now, admittedly, a bit funny and awkward, but hopefully this will be
by
ptaylor
-
AFNI Message Board
Ok, so you have two spaces of data for the same subject:
HARDI-imaged and DTI-imaged. They have difference spatial
resolutions, and my guess is that the physical locations might
not *exactly* overlay on top of each other. If the physical
locations exactly do overlay and you have the same field of view
for each set, then I guess resampling can work. The 3dAllineate
would be used to make a
by
ptaylor
-
AFNI Message Board
It appears that your -netrois FILE (i.e., your ROI network mask) is in a different space. You can map this to the other space (the one that the FA map is in) with something like 3dAllineate (assuming that a linear/affine mapping is fine) or 3dQwarp.
In the former case, when you apply the transformation to the -netrois FILE, then you should be able to specify `-final NN' for the nearest
by
ptaylor
-
AFNI Message Board
Ah, right, I have to update that error message.
That could refer to the netrois file or to the uncert file having different number of voxels than the FA map.
if you do
$ 3dinfo -nijk /home/laura/Desktop/DTI_NEW/PDD_ROIs/ROI_MASHUP.DIL5+tlrc
$ 3dinfo -nijk MND110.o.UNCERT.V2_UNC+tlrc
$ 3dinfo -nijk MND110.HARDINL.V2_FA+tlrc
do you get the same number output for all?
--pt
by
ptaylor
-
AFNI Message Board
If this build is for Ubuntu (version >=11/04, and 64 bit; might even be ok even back to version 10.*, but I'm not sure), then perhaps you could build from source using the suggestions in the text file:
afni_src/other_builds/OS_notes.linux_ubuntu_12_64
There's a list of things to `sudo apt-get install' which have been needed on Ubuntu from past experience-- the file itself is
by
ptaylor
-
AFNI Message Board
Hi,
Does anyone have experience with dealing with ghosting (specifically, "N/2 ghosting" or EPI-ghosting) in RS-FMRI with afni_proc.py? There are some odd artifacts (obviously). It seems like blurring early (and often?) is one way to deal with it. But are there any fancier techniques?
Thanks,
pt
by
ptaylor
-
AFNI Message Board
And if I understand correctly, then perhaps to do it all in one step from the start, by making use of `ispositive( )' in order to not get any negatives:
$ 3dcalc -a ROI_FS_rh.aIns.nii.gz -b Yeo_17Network_salience1_orig.nii.gz -expr '(a-b)*ispositive(a-b)' -prefix rh.aIns_fsROI.nii.gz
That way, the regions in which b>=a get a zero value; and for your specific example, it
by
ptaylor
-
AFNI Message Board
Well, it's hard(impossible?) to definitively compare methods in most cases. To quote from Cox (2011, NI), "What a long strange trip it's been":
<< Does it make sense for there to continue to be a number of highly overlapping open-source software packages for analysis of FMRI data-sets? Each software package for FMRI is not just a set of tools, but is also a social e
by
ptaylor
-
AFNI Message Board
Hi,
Ubuntu and Fedora are Linux flavors which are non-standard for AFNI-- i.e., they are not fully supported for compiling, and importantly the distribution doesn't come with a Makefile for them. Nonetheless, a number of people use these builds, and there is a feeling that it's unnecessary for everyone to keep reinventing the wheel by frustratingly fighting error messages during at
by
ptaylor
-
AFNI Message Board
Ok, thanks.
And ever since the `-h_view' option became available, I just can't *stop* reading the helpfiles.
--pt
by
ptaylor
-
AFNI Message Board