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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
Hi, Philipp-
Many times we use 3dinfo on just a single dataset as input. The command I gave you should be run on multiple datasets at once. Can you please run:
3dinfo \
-same_all_grid \
-prefix \
Extracted_ACW_Awake.nii Resample_Yeo7N_1000ribbon.nii \
DSET2 \
DSET3 \
....
where you fill in all your other datasets being used?
thanks,
pt
by
ptaylor
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AFNI Message Board
Hi, Philipp-
Maybe the best place to start is running this:
3dinfo -same_all_grid -prefix DSET1 DSET2 DSET3 ...
on all the dsets you are extracting data from and writing. That will point out where you have a mismatch of grids.
--pt
by
ptaylor
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AFNI Message Board
Hi, Fernanda-
It would help to see the 3dClusterize commands you are using. There shouldn't be anything stochastic/random in the algorithm to cause underlying variability. Are you certain that you are using the exact same threshold (you can rightclick the Thr above the colorbar, and select "Set threshold" or "Set p-value" directly by typing for example) and parameter
by
ptaylor
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AFNI Message Board
That is great that you could update the local AFNI, and the name of the program is:
@djunct_overlap_check
(not @adjunct_overlay_check). Please see if that works?
--pt
by
ptaylor
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AFNI Message Board
Hi-
Can we see how the original EPI and anatomical data (no changes to obliquity) overlay when you run this command:
@djunct_overlap_check -ulay DSET_ANAT -olay DSET_EPI -prefix check_olap
? That should create 2 images: one with obliquity *ignored* (which will likely have poor overlap) and then one where all obliquity is applied (called *_DEOB*). The question will be, how well do the data
by
ptaylor
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AFNI Message Board
Howdy-
One thing to note at the start, if you are putting your data into afni_proc.py, I wouldn't worry about deobliquing the EPIs. You can let afni_proc.py deal with it appropriately for you. (Perhaps you would want to deoblique the anatomicals, in a manner discussed below.)
There are 2 meanings of deoblique, with distinct consequences in either case.
+ "3dWarp -deoblique"
by
ptaylor
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AFNI Message Board
Hi-
Let's say you have an atlas or ROI map DSET_ROI where the amygdala is defined wherever that dataset has a value 4, and it could also have a label attached like "Amygdala". You can use the "-mask .." option and sub-range selector to focus on just that ROI and its time series:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/afni_gen/files_gen.html#sub-rang
by
ptaylor
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AFNI Message Board
3dpc is the program for that:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/alpha/3dpc_sphx.html#ahelp-3dpc
Using "-pcsave .." determines how many are output.
--pt
by
ptaylor
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AFNI Message Board
Hi, Shinyoung Jung-
Typically, one wouldn't directly align a statistical dataset to a template, because they statistics map doesn't have clear anatomical features (the kinds of data contained there are effect estimate and statistics blobs that might extend over structural boundaries).
For FMRI, during processing prior to statistical mapping, we might align the subject EPI to the
by
ptaylor
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AFNI Message Board
Hi-
I believe the issue is that the Python programs are referred to with "python", not "python3". Could you please try copy+pasting the following in a terminal:
ln -s /usr/local/bin/python3 /usr/local/bin/python
so that the command "python" will link (or essentially point) to what is called "python3".
If you then open a new terminal, does "af
by
ptaylor
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AFNI Message Board
Is this what you want:
3dinfo -labeltable MNI_Glasser_HCP_v1.0.nii.gz
or
@MakeLabelTable -labeltable_of_dset MNI_Glasser_HCP_v1.0.nii.gz
?
-pt
by
ptaylor
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AFNI Message Board
Hi, Jef-
OK, so my reading of this is that you are interested in building a pipeline for your EPI and anatomical T1w dataset, and that you want to use a standard space/reference template for the final location of the EPI data. Sounds great.
The obliquity "issue": so, for historical reasons, AFNI will (at present) vociferously warn about obliquity. This really is not that big a
by
ptaylor
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AFNI Message Board
... and as a follow-up, Gang provided a sage observation here to solve my conundrum about the third set of differences:
There are two subvolumes that can be used here: the "-idat .." and the "-ithr .." ones. This is because with something like a t-test, we often have both an effect estimate and an associated statistic from the modeling here---in general, both should be used
by
ptaylor
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AFNI Message Board
Hi-
Note that the cluster maps themselves are identical, as given by the 3dDiff command above, which is good.
The only values in the table that appear to differ relate to using the values themselves; most/all of these would be expected to be different:
+
CM values use the absolute value of the voxel values as weights.
... so any of the CM columns will likely differ.
+ the Mean, S
by
ptaylor
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AFNI Message Board
Hi, Jef-
OK, we can look into this. It may be the initial overlap is not very good, and/or that the tissue contrast or level of detail is mismatched.
A couple background questions:
A) Your input dataset already been warped once? I'm guessing this by the filename. I'm a little curious why there might be multiple warps/alignments? That might be fine, but each regridding can b
by
ptaylor
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AFNI Message Board
As a follow-up, I might note that having Enorm censoring at 0.2 or 0.3 (which are in units of ~mm) would be more typical, and outlier frac of 0.05 (= finding spots where a brainmask has 5% or more outliers).
I think you still have plenty of degrees of freedom to give, and this shouldn't result in too much time point loss, just eyeballing these motion plots. Hopefully that will reduce som
by
ptaylor
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AFNI Message Board
That is interesting about the EPI-anatomical alignment, and surprising. But if the alignment is working for you now, great.
Your censor thresholds, Enorm>1.0 and outlier_frac > 0.15, are higher than I have typically seen. From looking at the 1D profiles in the motion QC block, I would say there is some leftover motion artifact in the data, esp. in the first attachment. Some of that will
by
ptaylor
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AFNI Message Board
Hi-
Is that data already in Talairach or MNI space, or is the +tlrc there just because of some qform_code/sform_code value from whatever program did the OC?
Also, I'm curious if is there a particular reason you don't want to input the ME-FMRI data into afni_proc.py, and do the OC within it?
--pt
by
ptaylor
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AFNI Message Board
Hi-
Ah, I see, I misunderstood previously.
Could you please put your 3dBlurToFWHM command here? (And also just to check: I guess you aren't running this as part of afni_proc.py, is that right, but separately?)
I note that 3dBlurToFWHM does take some additional parameters for outputtng ACF parameters, such as these:
3dBlurToFWHM
by
ptaylor
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AFNI Message Board
Hi-
This is what the afni_proc.py command runs for residuals typically:
3dFWHMx \
-detrend \
-mask mask_epi_anat.$subj+tlrc \
-ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D \
by
ptaylor
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AFNI Message Board
Hi, Ian-
So, I assume your afni_proc.py (AP) command uses:
-align_unifize_epi local \
is that right? We recommend that now in most cases (at least for scans of humans) to deal with brightness inhomogeneity in the EPIs. Actually, the reason we don't necessarily recommend it in animal scans at present is because the skulls/nonbrain mat
by
ptaylor
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AFNI Message Board
Hi-
OK, so the issue does appear to be that: the F-stat clusterizing misses out on signedness, which the bi-sided clusterizing with the t-stat uses. Running 2-sided clusterizing with the t-stat gave the same results as the F-stat clusterizing.
Here were the 3 clusterize commands via the command line (and I use the 1sided ->right tail clusterizing on the F-stat, which would be the same
by
ptaylor
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AFNI Message Board
Thanks for that full output.
I am now running this command with "-child_epi .." and "-tshift_opts ..", and still not getting an error:
align_epi_anat.py -verb 5 \
-anat FT_anat+orig.HEAD \
-epi pb00.FT.r01.tcat+orig.HEAD \
by
ptaylor
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AFNI Message Board
Hi, Will-
Hmm, weird. I ran this similar command (just didn't have followers and ts_shifts, but those should not affect this) and did not get the same error:
align_epi_anat.py \
-anat FT_anat+orig.HEAD \
-epi pb00.FT.r01.tcat+orig.HEAD
by
ptaylor
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AFNI Message Board
Hi-
OK, the bi-sided vs 2-sided is selected in the initial Clusterize GUI that pops up; in this case, it won't have any effect on the F-stat, because it is always >=0.
I do think the difference is the t-stat is signed and clustered bi-sidedly; the F-stat is only positive, and can't distinguish between underlying positive and negative effects. Consider in the t-stats when the
by
ptaylor
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AFNI Message Board
Aye, there's the rub. Some available ones have artificial brightness patterns and things.
I might try out these MNI McGill infant templates:
https://nist.mni.mcgill.ca/infant-atlases-0-4-5-years/
to start. I am a little surprised they are not sharper/crisper. The package name is a bit confusing, I think, since they don't have reference atlases (= ROI maps) associated with them,
by
ptaylor
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AFNI Message Board
Hi-
Thanks, I thiiiink I see the issue, and I noticed this looking at the top text rows of your cluster report. And thanks for including the 3dClusterize commands.
The F-stat here should be equal to t-squared---fine. There will be a bit of rounding difference, which might affect some thresholding, but that should be minimal. In each case, AFNI should be able to translate a given p-value
by
ptaylor
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AFNI Message Board
Neonates and infants should likely have a different reference template---often their scans have different contrasts/properties, even in structural imaging.
For children, say, 4-5 and older, the Haskins might be the closest available, and also will become increasingly age-matched over the duration of your scanning, as well. It would also help with consistency over much of the age span.
--
by
ptaylor
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AFNI Message Board
Howdy-
Hmm, OK.
This line in the system check output (and thanks for including that from the start!):
release: 5.10.16.3-microsoft-standard-WSL2
... makes me think that it is WSL2 that you have, instead of WSL1.
These are some notes on things sent by an AFNI user, Joel Stoddard:
+ From here: https://learn.microsoft.com/en-us/windows/wsl/tutorials/gui-apps#existing-wsl-install
by
ptaylor
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AFNI Message Board