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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
Results 1351 - 1380 of 2305
Hi, Paul-
For aligning to a template space, as well as for skullstripping an anatomical, we have started to recommend using @SSwarper before running afni_proc.py. There is an example of using that warpage information in your subsequence afni_proc.py command in the @SSwarper help file.
For aligning EPI and anatomical, we still recommend using the lpc+ZZ cost function (I'm not sure if
by
ptaylor
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AFNI Message Board
Hi, Shun-
Hmm, OK, well if you have got the R packages installed, then that's great.
If you are also asking about that message/notice at the bottom of the afni_system_check.py output, then:
It's not something that requires you to do anything. It refers to the fact that many times when we reply to questions on the MB or put examples online, we use "tcsh" shell syntax de
by
ptaylor
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AFNI Message Board
Hi, Korann-
I'm not sure of what file is being shown. What file name is this?
Note that transforms are calculated for individual steps across space, but they are not applied individually. Those transforms are concatenated and then applied as a single transform on the original data (EPI).
--pt
by
ptaylor
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AFNI Message Board
Hi-
I am sorry, but I'm not sure. I've tried it on my system, and things worked.
I removed R with:
sudo apt-get remove r-base-core
Then, this is what the end of my /etc/apt/sources.list file looks like, if that is useful (though, note that this forum format will change the full links to the abbreviations, that you will have to see by clicking on them):
## Uncomment the
by
ptaylor
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AFNI Message Board
Hi, Sarah-
The lines are of the volume, made using 3dedge3-- they show where the contrast is changing a lot. The colorbar is Plasma, with yellow showing the largest changes in contrast (hence it is usually at the edge of the brain) and violet/purple showing the smaller differences.
The images are of the template (that you choose) and anatomical brain, yes, in the following representations:
by
ptaylor
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AFNI Message Board
Hi,
I think there should be a space between "ubuntu" and bionic-cran35 in the uncommented deb line; unfortunately, this interface turns links into abbreviations, but it should look like the following with the underscores "_" removed:
deb h_t_t_p_s_:_/_/cloud.r-project.org/bin/linux/ubuntu bionic-cran35
Try copy+pasting that and replacing the current link (or adding t
by
ptaylor
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AFNI Message Board
Hi, Shun-
I believe that you should first remove R, because otherwise there are version conflicts. Then,
1) open the "list" file of sources for your package manager (sudo/admin password required):
sudo gedit /etc/apt/sources.list
2) Copy+paste this line to the bottom of that file (this gives your package manager a new place to look for files to install- specifically, R v3.5
by
ptaylor
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AFNI Message Board
Hi, Shun-
Thanks for sending that. I think that, indeed, you just need to update your R version. To do that in this case, you should be able to do the following
---- EDIT: well, actually wait, this appears to not have sorted things; watch this space for a better answer hopefully shortly.... ---------
-pt
by
ptaylor
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AFNI Message Board
Hi, Shun-
It is hard to say without knowing more about what operating system you are using.
What is your output of:
afni_system_check.py -check_all
?
I believe that version of R is not modern enough, but please copy+paste the output of the above command.
--pt
by
ptaylor
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AFNI Message Board
Hi, Korann-
Great, glad that worked out.
Indeed, the @SSwarper tool that Bob wrote is pretty new, and we are trying to integrate it more into documentation as we have used it and grown more comfortable using it. It is a challenge to keep uptodate with recommendations and new programs. Actually, pretty soon we intend to put more processing examples online. And we would recommend that all
by
ptaylor
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AFNI Message Board
Hi, Korann/Vittal-
This syntax doesn't look quite right; I think it is missing a "-input ..." option name. I think this is what you would want (and just spaced one per line, for readability):
@SSwarper \
-input CSRI-004-1-Structural.nii \
-base MNI152_2009_template_SSW.nii.gz \
-subid CSRI004 \
Note that in this m
by
ptaylor
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AFNI Message Board
Hi, Korann-
Well, indeed, cat_matvec shouldn't be trying to combine 1D text file with a volumetric data set...
One thing is that you should pass skullstripped anat with "copy_anat", and then tell afni_proc.py that you have already skullstripped the brain:
-copy_anat anatSS.${subj}.nii
-anat_has_skull no
where ${subj} stands for where your subject ID would be. You can sti
by
ptaylor
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AFNI Message Board
Hi, Lz-
The description of vox_to_ras in the TRK header definition is:
"4x4 matrix for voxel to RAS (crs to xyz) transformation. If vox_to_ras[3][3] is 0, it means the matrix is not recorded. This field is added from version 2."
In 3dTrackID, the vox_to_ras 4x4 matrix is initialized to all zeros, which is a valid value, and then it is changed nowhere in the code.
While this
by
ptaylor
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AFNI Message Board
Hi, Korann-
I'm a little confused by what your actual afni_proc.py command was that, running, gave you an error message. Could you please copy+paste just that? You can separately include the lines you have removed, if you wish. Note that you will need to include:
-tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp
by
ptaylor
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AFNI Message Board
Hi-
A few quick questions:
1) are you using afni_proc.py, or doing something separately?
2) What is the output of:
afni_system_check.py -check_all
?
3) What is the output of:
3dinfo -n4 -o3 -orient -prefix deoblw_pb06.shellgame_26.r02.Cd3MP+orig shellgame_26.BrainExtractionBrain.nii.gz
4) what "other" EPI are you using that makes things OK?
--pt
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ptaylor
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AFNI Message Board
Hi, Sam-
Plans: yes.
Time: ummm.... more difficult.
Hopefully we will someday, indeed!
--pt
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ptaylor
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AFNI Message Board
So, running "afni" still gives you an error message? Can you run:
afni_system_check.py -check_all
and copy+paste the full results?
Also, just to make sure-- did you double click the VcXsrv icon on your desktop *before* starting the Ubuntu terminal session?
--pt
by
ptaylor
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AFNI Message Board
Hi, Korann-
A few things there.
What is your AFNI version ("afni -ver")? If it is quite recent, then you should get a directory called QC_ (in your case, probably QC_INSP004) that would have a full report of quality control (QC) blocks from your afni_proc.py processing. This is described in detail here:
It will show you individual alignment step results (EPI to anat, and an
by
ptaylor
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AFNI Message Board
Hi, Sungjin-
After running those suggested changes, when you start your VcXsvr and then open a new terminal, what is the output of the following:
echo $DISPLAY
?
by
ptaylor
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AFNI Message Board
Hi, Sam-
Using ZERO in 3dTproject would not be good enough. The issue is that the typical way of estimating spectral power (or amplitude) distributions is via the Fourier Transform (FT, or Discrete Fourier Series (DFT)). To use the FT, the time series data must be regularly sampled. Inserting zeros means that the length of time series doesn't change, but those would be interpreted as v
by
ptaylor
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AFNI Message Board
Hi, Sam-
You can't combine censoring and 3dRSFC.
At present, the best way to go to estimate RSFC parameters like ALFF, fALFF, RSFA, etc. if you are censoring would be to use 3dLombScargle (yes, that's really the name of a program) with 3dAmpToRSFC after. 3dLombScargle can estimate a power spectrum when the sampling rate isn't constant (i..e, when FMRI data sets have been cen
by
ptaylor
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AFNI Message Board
Hi-
Probably the best way to output a region from a known atlas, rather than drawing something that exists, would be to dump it to a file directly using AFNI's program "whereami".
Here is an example of doing that for the Left BA 47:
whereami -mask_atlas_region TT_Daemon:left:Left_Brodmann_area_47 -prefix lh_ba47.nii
right BA 74 (using a slightly different syntax to above
by
ptaylor
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AFNI Message Board
Hi again-
[**EDIT**: this suggestion does *not* actually give a data set, I was mistaken; this just outputs a text file listing which regions are being colorized (or are 'None'). See the reply to this email for a better, automatic way to output the desired region mask directly from the commandline.]
Also note that if you are just literally re-drawing the BA-27 region, you can us
by
ptaylor
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AFNI Message Board
Hi-
I'm not sure. I've just PM'ed you instructions on how to upload the dset, if you'd like me to take a look.
--pt
by
ptaylor
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AFNI Message Board
Hi, Galit-
Glad that sorted it.
And no worries, those are find intuitions and good questions. The linear (affine) transformation describes the mapping rules between sets of points. The grid itself is separate-- that establishes the field of points themselves (that are pulling data from the source grid).
There is matrix multiplication going on. If the source and master dset were both c
by
ptaylor
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AFNI Message Board
Hi-
Right now, your $DISPLAY variabile is not set in your system. Can you please do step #4 here (copy+pasting a few commands into the terminal) and then open a new terminal to try again:
?
That should set up your terminal $DISPLAY variable. Note that Step #3 there describes how to set up easier copy+paste capability on the Windows Subsystem Linux. Note also Step #2 that describes how t
by
ptaylor
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AFNI Message Board
Hi, Ilaria-
Yes, netpbm is required as part of the AFNI install-- please see here to get it:
Hope that sorts it out.
--pt
by
ptaylor
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AFNI Message Board
Hi-
There is a bit of tutorial for working with ROIs (combining them into files, making surfaces for viewing, attaching labels, and more) here:
For your case specifically, it seems like you already have ROIs defined in a file-- each ROI is defined as being a set of voxels with a given integer (NB: each ROI need not be contiguous, as I would guess is the case for your example). In your ca
by
ptaylor
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AFNI Message Board
Hi, Galit-
Can you please post your 3dAllineate command and align_epi_anat.py commands here?
Note the "3dAllineate -1Dmatrix_apply ..." will apply the specified aff12.1D file, but as to the final grid of the output, that depends on the "-master ..." dset.
In order to specify grid resolutions for align_epi_anat.py, there are these options (and you should check out th
by
ptaylor
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AFNI Message Board