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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 181 - 210 of 2305
Howdy-
I'm a little confused. Did you first run afni_proc.py, and now you are separately running align_epi_anat.py in the same directory? If so, I was wondering why you are running this separately, after the analysis is complete?
Separately, in this line of the afni_proc.py command:
-align_opts_aea -cost lpa -cost lpa+ZZ -giant_move \
... "-cost .." should not be specifi
by
ptaylor
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AFNI Message Board
Hi-
Is that the full "afni_system_check.py -check_all" output? There should be a lot more information at the start. I can see that you are using a Mac, but I can't see what version. There are notable issues with not having XQuartz.
I think you should check the installation items for your Mac OS version here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_instal
by
ptaylor
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AFNI Message Board
Howdy-
Just to note, all the colorbars are listed here, in action:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/afniandafni/all_afni_cbars.html
To make a local colorbar (or "palette"), you can see what the format would look like as follows:
+ open the afni GUI
+ load some overlay or click on "Define Overlay"
+ right-click on the "Olay" above the colorbar
by
ptaylor
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AFNI Message Board
You could use p2dsetstat to get the desired threshold for volume AAA in the original DSET_WITH_INFO, for a given pvalue PVAL, say for a bisided stat:
p2dsetstat \
-bisided \
-inset DSET_WITH_INFO"" \
-pval PVAL
... and then you could use that threshold value directly within your warped dset.
--pt
by
ptaylor
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AFNI Message Board
Hi, Lysianne-
Indeed, the "p= ..." convenience comes about only from AFNI-program-produced stats, which stick the conversion information into the header.
What is the 3dClusterize command you are using, and where did the stats dataset come from?
--pt
by
ptaylor
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AFNI Message Board
Hi, Lysianne-
You can make idat and ithr just both point to that [0]th volume:
3dClusterize -idat 0 -ithr 0 ...
--pt
by
ptaylor
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AFNI Message Board
Hi, Asya-
You should be able to have the quality control HTML on any system. Can you please provide the output of:
afni_system_check.py -check_all
?
If I understand the images you have posted correctly, it looks like the anatomical dataset has the wrong header information: in what should be axial slices, the dataset looks like a rotated sagittal view. Is that what it looks like before
by
ptaylor
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AFNI Message Board
Howzabout this elegant combination of AFNI and shell commands:
3dROIstats -quiet -mask DSET_INT DSET_INT | tr '\t' '\n' | awk '{print int($1)}'
... which, in turn, get the mean value of each ROI region (which produces a line of floating point values of the ROI integers); which gets turned into a vertical column of those floating point values; when then get integ
by
ptaylor
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AFNI Message Board
Hi, Asya-
In your output "results" directory from afni_proc.py, there should be a "QC_${subj}" directory, which contains the afni_proc.py quality control (APQC) HTML.
Can you go into that results directory, and type:
afni_open -b QC_*/index.html
.... to open the APQC HTML in your default web browser (or you can open that file in any browser you want).
Can you check
by
ptaylor
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AFNI Message Board
Oh, and I just assumed this was rebumping the question to remind me to answer...
Glad that my past self was more on-the-ball about reply, at least. Sorry for the delay, but glad you found the reply.
--pt
by
ptaylor
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AFNI Message Board
Hi, Sam-
I think that is unrelated to ANATICOR.
When "3dAllineate -allcostX ..." is run, that volumized* dset is created. It is local volume mask related to lp* cost functions, I believe.
--pt
by
ptaylor
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AFNI Message Board
Great, glad that sorted it and thanks for letting us know.
--pt
by
ptaylor
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AFNI Message Board
Hi,
Yes, we have updated the installation instructions for Ubuntu 22.04 here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu22.html
--pt
by
ptaylor
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AFNI Message Board
Hi-
I have updated the Ubuntu 22.04 installation instructions. The GSL linking has changed from Ubuntu 20.04, and should be:
sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.19
The updated list of dependencies is also on this page:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu22.html
--pt
by
ptaylor
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AFNI Message Board
Hi-
Thanks for posting that.
OK, I would update the align_opts_aea option (for controling anatomical-EPI alignment, AEA) to be:
-align_opts_aea -cost lpc+zz -giant_move -check_flip \
That is our general starting point---from the options you cited above, the "-giant_move" might be necessary to open up the parameter search space for the alignment. The "-check
by
ptaylor
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AFNI Message Board
Howdy-
I think the best way to go would be to paste your current afni_proc.py (AP) command here, and we can recommend tweaking options from there. The PyQt4 dependencies are really difficult nowadays. We have let uber_subject.py lapse because, in general, working with the AP script directly is clearly and easier to discuss, particularly on the Message Board here. (All uber_subject.py did wa
by
ptaylor
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AFNI Message Board
Hi, Lysianne-
The .aff12.1D and _WARP.nii transformations can be catenated to get the full warp from orginal space to the base space, such as in this example:
3dNwarpApply -nwarp 'anatQQ.sub007_WARP.nii anatQQ.sub007.aff12.1D' ...
As to this dset, I will send you a Box link, and I will at it more, if that is OK.
-pt
by
ptaylor
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AFNI Message Board
Hi-
What is the output of "3dinfo -obliquity DSET" on the dset that you put into 3dLME?
And I guess what is the output of this command:
nifti_tool -disp_hdr -infiles DSET
--pt
by
ptaylor
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AFNI Message Board
OK, thanks for sending that. That doesn't look too bad for the initial skullstrip, for making the initial alignment.
Please let me know how the lpa cost function works.
--pt
by
ptaylor
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AFNI Message Board
Hi-
Sure, that is fine, yep. I would guess that there are more files than FA output, such as the first eigenvector (what we might call "V1" in a filename)? For performing tractography, that would also be necessary.
--pt
by
ptaylor
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AFNI Message Board
Hi-
How about adding this option, to have lpa used as the cost function for the final rounds?
-cost_nl_final lpa
Note that the init_qc_01_nl0 is not the final nonlinear (NL) result, but the start of the main nonlinear part. That means that the first image there is showing that there will be a bit of ways to go. It is possible that the lpa cost, above, will help resolve the alignment at
by
ptaylor
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AFNI Message Board
Hi, Melissa-
Are you wanting to take N subject's 3D ALFF volumes, stack them together into a N-by-3D dataset, and then calculate the voxelwise normalized "Z" value of each, based on the voxelwise mean and standard deviation?
There are different ways to slice the data, and that matters for order of operations and program(s) used.
-pt
by
ptaylor
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AFNI Message Board
OK, thanks for working through that and for letting us know.
--pt
by
ptaylor
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AFNI Message Board
The voxelwise ALFF values are calculated with the following steps:
time series (detrended or not, chosen by user) -> FFT
For the denominator of fALFF:
- go through positive harmonics from m= 1 (ignore baseline harmonic) to Nyquist, and sum the sqrt of power per frequency (that is, sum the amplitudes)
For ALFF and numerator of fALFF:
- go through harmonics from m= minimum index to maximum
by
ptaylor
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AFNI Message Board
Hi-
Do you want the average time series per ROI? There are different ways to do this, but most will not make a "ROI=0" time series. The label is there, as every voxel has a label, though. I would probably use 3dNetCorr with one or more of the following options:
-ts_out :switch to output the mean time series of the ROIs that
have been used to gene
by
ptaylor
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AFNI Message Board
Hi-
The "extra" dimension there is because there is the following label:
"0" "Unknown"
So, it is not a problem. There are 4 header lines in the NIML-format output, so if you run:
3dinfo -labeltable MNI_Glasser_HCP_v1.0.nii.gz | wc -l
to count the number of lines output to the terminal, you get: 365. There are 3 "header" lines at the top, which
by
ptaylor
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AFNI Message Board
Ha, OK (or, as they say in Italy, OK).
Re. the correlation conundrum:
Ah, I see. Indeed, that is a bit tricky. So, you want region-to-voxelwise correlation, not within-network-of-regions correlation? Well, at least 3dNetCorr can output all the time series at once:
-ts_out :switch to output the mean time series of the ROIs that
have been used to generate
by
ptaylor
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AFNI Message Board
Ciao, Dante-
As always, a pleasure seeing you post here!
Re. 3dNetCorr and blurring:
I would say that you should not blur the data during processing. Let 3dNetCorr do the averaging of time series within each ROI for you (which it does internally). If you blur the data prior to that, you will likely artificially boost the correlations among neighboring ROIs, because they now share time se
by
ptaylor
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AFNI Message Board
Well, on second thought, that "-prefix .." idea is a bit tricky, because BIDS-formatted data have rigidly encoded filenames. So, by definition, the input dset will have to be replaced by the output, to maintain BIDSiness.
Will ponder a bit more.
--pt
by
ptaylor
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AFNI Message Board