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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:
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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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Assuming the oblique warning above is fine (since it's there, and the same, already for anat_final vs vr_min_outlier, I assume it's fine)...
Then the goal is to get the live nii file to overlap well with the vr_base_min_outlier (or I guess anat_final is also fine).
Now I have done nothing to obliquess in any dataset.
I only do this:
3dcopy ../../data/nii_1/1.nii 1
Generating 1
by
Robin
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AFNI Message Board
Thanks Rick. How scared should I be of warnings in the viewer and from 3dvolreg like:
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
If
by
Robin
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AFNI Message Board
Hi!
A)
I'll change
-blur_size SOMETHING
-anat_has_skull YES_OR_NO
To be explicit
B)
I'll remove
-regress_apply_mot_types demean deriv \
C)
Yes, I have realized that is a good idea. I'll change the first steps accordingly:
# Once the TR is registered
cd $afni_dir/all_TRs
name=TR$last_brik
mkdir $name
cd $name
#changing this
cp $nii_dir/${last_brik}.ni
by
Robin
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AFNI Message Board
Note: ptaylor split this message off from this thread:
... into this new one, because it starts a new/different topic (albeit related to alignment).
-------------------------------------------------------------------------------------------------------------------------------------
Thank you so much, we are running with the new prepp data and with and without -align_unifize_epi local \.
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Robin
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AFNI Message Board
Thanks Paul!
How well should the results from @djunct overlay images align?
Because these commands do not align them, but move them closer, right?
They do not perfectly overlap. See attached. Is this expected?
Thanks again!
EDIT:
These are not the problematic data, they are on a system I can't access right now. These data did work well with the old scripts.
But you can still see
by
Robin
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AFNI Message Board
Hi AFNI people!
We have a set of scripts that has served us well before, but we are now analyzing data from another lab and we have problems with the alignment of the EPI onto the anatomy.
Using tips we got from Paul Taylor we prepp our T1: data by first:
3dcopy T1_$subject.nii tmp
3drefit -oblique_recenter tmp+orig
3drefit -deoblique tmp+orig
3dcopy tmp+orig T1_do_$subject.nii
#3dZ
by
Robin
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AFNI Message Board
Thanks, an improving moco over time then :)
Haven't used AFNIs plugin. Does it use a listener on a specific folder to which the scanner sends the data?
I built my own engine using python with the watchdog library/function.
That triggers a chain of events every time a file is detected. And at specific TRs it runs an afni script that provides my a time course / results for whichever TRs I
by
Robin
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AFNI Message Board
Thanks Gang!
So there is no equivalence in AFNI to the ICA tools in Conn for example?
by
Robin
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AFNI Message Board
I'm not sure we will get any further. I'm sorry if things are unclear.
But I can't use the full time course.
Once we reach TR 27, live in the scanner, I want to instantly calculate the average (in an ROI) of TR 23,24,25,26.(index start at 0) and provde feedback to the subject. TR 23-26 is when the subject is watchig an image.
Best I can do is to use TR 0..26. Then, as you
by
Robin
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AFNI Message Board
Hello!
Silly question, but I have never used ICA for neither cleaning/de-noising or for analysis.
A post here from 2016 stated that AFNI did not have any ICA tools. But I did find that it now does:
This seems to be the AFNI version of doingICA de-noising. I.e. using ICA for pre-processing.
Does AFNI now have ICA for both pre-processing AND for analysis?
The sillyness of this ques
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Robin
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AFNI Message Board
I read your post again.
How can I use the entire timeseries to do the regresson if this is a live neuro feedback run?
Firstly, the first time we collect data is about 27 TRs into the run. The following TRs have not been generated yet. So I don't see how I can use the full run.
Secondly, if we did this but "backwards"
First time we calculate something: use TR 0 up until last
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Robin
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AFNI Message Board
Hi Rick!
That is not how I do it, but I can if you think that will help!
What we do now:
Time progresses, each scan/TR/epi is identified and stored.
When it's time for the subject to get feedback (the last TR to include in the calculation) the progam gets that TR and 12 TRs worth of history.
E.g. TR 14..27.
This BLOCK, as I call it, is volreged to the mask that we made in a previou
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Robin
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AFNI Message Board
Thanks Rick! Didn't even think about degrees of freedom. Makes so much sense.
The short story here then is that we cannot do motion correction if we for each block want to use the same number of TRs.
I could extend the blocks to each contain data for about 14 extra TRs (include the TR's left of the first red block until 0). Making the snipped 27 TRs long. I shoulnd't bother wit
by
Robin
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AFNI Message Board
Hello AFNI folks,
I noticed something when trying to implement an AFNI-based real time fMRI engine that I made.
To trouble shoot I collected all EPI files after the run and stitched them together into a full 4D run.
Using the full run I used 3dvolreg to align it to the EPI containing the mask from where we would like the feedback. For trouble shooting purposes I used visual cortex to get
by
Robin
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AFNI Message Board
Thanks Gang!
Is it the number of sub-briks in the results output (i.e. depending on the stats used in 3dMVM) or is it the number or sub-briks in the residuals (number of subjects)?
In any case, I tried it and it does not work.
I installed a fresh AFNI install, to avoid any of my old edits.
I then found the lines:
print(sprintf("Start to compute %s slices along Z axis. You can monit
by
Robin
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AFNI Message Board
Thansk Gang,
I liked this:
> Alternatively, in this case, you can temporarily comment out those few lines in 3dMVM.R that performs model checking, and then run 3dMVM on those first and last 10 slices
Do you mind helping me identifying those lines?
It was not these (line 1558-1569)
# pick up a test voxel
if(!is.na(lop$maskFN)) {
idx <- which(lop$maskData == 1, arr.ind = T)
by
Robin
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AFNI Message Board
Thanks!
This was on a computer that I'm not managing, made them update the binaries and now it works! Thanks RIck!
I have a related question, I will try to make it clear - It might by difficult, haha.
Task: Run 3dMVM on a huge number of datasets. Getting the stats: No problem, it does them slice by slice. Problem: using the -resid option. It keeps all images (4D) in memory.
The s
by
Robin
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AFNI Message Board
Hi again Gang!
I wanted to try this. We are using a different dataset but again, it is quite large (7450 dual-regression maps). I'm using MVM and to find out significant cluster sizes vs per-voxel-pvalues. I need the residuals to be able to run 3dclustsim. 3dMVM finishes but fails at creating the the residuals (could not map memory).
I wanted to split the the images, like you suggested
by
Robin
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AFNI Message Board
Thanks a lot Rick! (again)
We are OK with some interpolation/smoothing. We aim to throw 20k+ brains at a 3D CNN and want to see if we get similar results with smaller grids.
We ended up using 3dresample -dxyz 2.0 2.0 2.0. Since all volumes have 1x1x1 mm or values very close to this we expect everyone to end up with 104x128x128 grids. So far so good. I'll let you know once it finishes =)
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Robin
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AFNI Message Board
Hello!
I can't figure out how to simply resample my images with 50% in each dimension!
I have a huge set of T1 images that I want to use in deep learning. To reduce the disk-usage we want to try and resample/shirk the matrix dims.
Example image:
R-to-L extent: -108.364 -to- 98.636 -step- 1.000 mm [208 voxels]
A-to-P extent: -123.597 -to- 131.403 -step- 1.000 m
by
Robin
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AFNI Message Board
Thanks Rick! That answered all my questions at once!!
I am trying to replicate the AM results a collegue did in SPM since the other fMRI-tasks has been analyzed in AFNI we want to keep it concistent in the paper.
I am no SPM person and I assume you guys don't know it super well either(?). So regarding the durations: I was told it was an event design, and you just tell SPM that. I am tr
by
Robin
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AFNI Message Board
Also:
After running freesurfer + @SUMA_Make_Spec_FS:
@SUMA_Make_Spec_FS -sid $subject -NIFTI & PIDT2=$!
I do get all files asked for in the script apart from one. This is the afni_proc.py documentation code:
-anat_follower_ROI FS_wm_e epi SUMA/mask.aseg.wm.e1.nii.gz \
-anat_follower_ROI FS_REN_epi epi \
SUMA/aparc+aseg_RE
by
Robin
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AFNI Message Board
Hi AFNI-sages. It was a while ago I ran amplitude modulation analysis in AFNI. I have a few questions to make sure I'm doing it right. Thanks in advance!
First assumation: This is the exampel to look at in the afni proc documentation:
Quoteafni_proc
NARPS. Applied NARPS example from AFNI. ~2~
(recommended? yes, reasonable for a complete analysis)
A
by
Robin
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AFNI Message Board
>>It seems that the memory crash happened when 3dMVM was trying to save the results to the output file. One easy solution is to break the input files into a few >>chunks. For example, suppose there are 90 slices along the Z-axis, use 3dZcutup to create 3 separate files: one for slices 1-30, one for 31-60, and one for >>61-90. Do this in a loop for all the input files. Then run 3
by
Robin
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AFNI Message Board
Thanks Gang!
I'm just thinking out loud, maybe this is unreasonable. Big data is getting more and more popular. It's not rare to run statistics on between 2000-10000 subjects. 3dMVM seems to able to run huge datasets, but the internal function -resid can not. And this is even on a 500 GB RAM system. Larger systems are rare.
Are you planning on updating the functionalities in the f
by
Robin
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AFNI Message Board
Hi again,
Running 3dMVM on a 500 GB RAM system. I can't tell if this is a memory (RAM) issue or something else.
3dMVM with -resid has worked before on this server with about 1800 subjects. Now I'm running with 2700 subjects. The results files are generated but not the residuals. I get this error:
*** caught segfault ***
address 0x7f79f8cbf820, cause 'memory not mapped
by
Robin
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AFNI Message Board
Hello!
When running 3dmvm with the -resid option having a large dataset (somehwere over 1500 subjects when having about 125 GB of RAM) it crashed due to memory error. I think it's R that complains, I saw a smilar post here that said it was memory issues.
The stats are generated but not the residuals, so I am fairly sure that it's the -resid part that crashes.
Would it be reason
by
Robin
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AFNI Message Board
Hi!
To clarify:
When running the command I get:
results+tlrc.BRIK and results+tlrc.HEAD (expected)
residual+tlrc.BRIK and residuals+tlrc.HEAD (expected)
The residuals file has 1800 sub-briks (expected since we have 1800 subjects and we get one sub-brik in resduals+tlrc per subject)
The results file has 1804 sub-briks (not expected).
After comparing I now see that the first 4 sub-briks
by
Robin
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AFNI Message Board
Thanks Gang, a final question:
I ran 3dMVM using a merged 4D volume with the vbm-gray-matter-modulated volumes of all 1800 subjects:
3dinfo ../GM_mod_merg.nii.gz
++ 3dinfo: AFNI version=AFNI_21.0.12 (Feb 25 2021) [64-bit]
Dataset File: ../GM_mod_merg.nii.gz
Identifier Code: NII_FIGEgKOgUVe0sJpMi6fe6A Creation Date: Thu Sep 23 11:08:02 2021
Template Space: TLRC
Dataset Type:
by
Robin
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AFNI Message Board
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