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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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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.
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Hey,
I have EPI data with three echos. When I load these files into AFNI and open a new controller for each of the three echos, I can clearly reduction in the brightness of the data for each of the three echos. This is clearly shown in this image In this image echo 1 is the first row, echo 2, the second and echo 3 the final row.
I'm making images of each slice (for each orientation :
by
Colm Connolly
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AFNI Message Board
I'm running it with bash.
I just eliminated the backslashes from the GLT specifications and reran it. Now I only get one coef and tstat per GLT as expected.
I never knew that a GLT could have more than one line in the contrast matrix so never suspected that the backslashes would be the culprit.
Thanks for you help, Rick. Much appreciated.
by
Colm Connolly
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AFNI Message Board
Hi everybody,
I have a problem which I've never seen before. I have the script below used to directly run 3dD.
3dDeconvolve -input $fmriprepdir/sub-${subj}_ses-${ses}_task-CCT_run-*_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz \
-jobs 8 \
-polort 4 \
-float
by
Colm Connolly
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AFNI Message Board
Have you tried dcm2niix_afni included with AFNI or Chris' Rorden's dcm2niix?
by
Colm Connolly
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AFNI Message Board
Thanks! I figured there'd be more than one one way to do this in the Swiss army knife that is AFNI!
by
Colm Connolly
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AFNI Message Board
Hey,
Given a integer valued data set (e.g., a mask), what's the most straightforward way to get a list of the unique values in the data set?
Regards,
Colm.
by
Colm Connolly
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AFNI Message Board
You need to resample the mask so that it is on the gridset as the functional data.
3dresample is one program that can do this for you.
3dresample -master func_task_pp_ICAaroma_bptf.nii.gz -prefix SN_resam.nii -input SN.nii
here the -master dataset is the one you want to match.
3dfractionze can also do this and will give you much more control over process.
by
Colm Connolly
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AFNI Message Board
Check that the TR is correct in the input EPI volume(s), in this case ${funcdir}/${subj}_Stroop_Run01.nii
3dinfo ${funcdir}/${subj}_Stroop_Run01.nii
you can get lots more info (more than you need to check the TR) by instead running
3dinfo -verb ${funcdir}/${subj}_Stroop_Run01.nii
by
Colm Connolly
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AFNI Message Board
You are looking for what are called married regressors. Have a look at and search for married.
In brief, each event in a regressor will consist of onset:duration pairs, e.g., for an event that starts at T=2s and lasted 1.2s you would encode this as 2:1.2. In afni, regressors are entered in text files with one line per run and multiple events within a run separated on a line by spaces. Runs wi
by
Colm Connolly
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AFNI Message Board
Hey,
I'm trying to invoke afni using the -bysub argument to read in a bids dataset of my creation.
I'm running afni as follows
afni -bysub sub-117 - ./
In this case ./ contains the derivative/sub-XXX/ses-YYY/{anat,func}/sub-xxx_ses-YYY_{T1w,task-rs_bold}.nii.gz files.
Afni complains as follows and only shows the MNI brain with apparently no datasets read in:
$ afni -bysub
by
Colm Connolly
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AFNI Message Board
You do not need the -b variable:
for bash: 3dcalc -a betaCoefficients.nii.gz -b -expr 'a/$( cat referneceValue.1D)' >normalized betas.nii.gz
for tcsh or bash: 3dcalc -a betaCoefficients.nii.gz -b -expr 'a/`cat referneceValue.1D`' >normalized betas.nii.gz
This assumes that there is one and only one properly formatted number in referneceValue.1D
by
Colm Connolly
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AFNI Message Board
I no longer have the dataset. By now it would be 10-15 years old. You could probably simulate it quite well by adding salt and pepper noise to an existing dataset. A median filter cleaned it up very effectively.
by
Colm Connolly
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AFNI Message Board
I had a similar problem with very noisy data acquired on a 3T scanner. I ended up having to clip as much of the non-head regions of the T1 images so that the noise would not pull the mask outside the head. I used @clip_volume to zero this out. In the AFNI viewer, load in your T1 and make a note of the six x, y, z planes that get you as close to the head as possible and then create, possibly multi
by
Colm Connolly
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AFNI Message Board
Hi,
Quick question about LABELs in afni_proc.py. If I pass the following arguments to afni_proc.py
-anat_follower_ROI aaseg anat ${SumaDir}/aparc.a2009s+aseg.nii \
-anat_follower_ROI aeseg epi ${SumaDir}/aparc.a2009s+aseg.nii \
-anat_follower_ROI FSvent epi ${subject}_vent.nii \
-anat_follower_ROI FSW epi ${subject
by
Colm Connolly
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AFNI Message Board
Hey,
Could the code at the top of @SSwarper that sets OMP_NUM_THREADS based on CPU resources allocated in queueing system be modified (as follows) to work with GridEngine as well as SLURM?
# set number of threads if run via SLURM or Grid Engine
if ( $?SLURM_CPUS_PER_TASK ) then
setenv OMP_NUM_THREADS $SLURM_CPUS_PER_TASK
else if ( $?NSLOTS ) then
setenv OMP_NUM_THREADS $NSLOTS
en
by
Colm Connolly
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AFNI Message Board
Gang,
I've been running RBA as follows:
if [[ ${laterality} == "unilateral" ]] ; then
graphLayout="3 6"
elif [[ ${laterality} == "unilateral" ]] ; then
graphLayout="4 5"
fi
RBA \
-prefix ${laterality}.${glt}.rba \
-chains 4 -iterations 1000 \
-PDP ${graphLayout} \
-Subj Subj -ROI ROI -Y contrast \
-cVars &
by
Colm Connolly
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AFNI Message Board
Excellent, Gang, thanks. I'd not noticed RBA.
If I may put the fox back in the hen house: I have more than one contrast, thus there will be multiple models suggesting a multiple comparisons issue. How does one deal with this in the context of the Bayesian approach.
I just skimmed the RBA help text, example 3 interaction suffers from teh same sign issue as MBA.
by
Colm Connolly
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AFNI Message Board
Hi,
I've been playing with BayesianGroupAna.py and would like to perform the equivalent of a between group t-test. Is this possible? Having read the paper, it would seem that it should be theoretically possible.
The example analysis in the paper describing the rational for BayesianGroupAna.py, operationally defined brain activity as the Z scored correlation between a seed and the other
by
Colm Connolly
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AFNI Message Board
I guess this one is for Peter: Would it be possible to add a -weights option to 3dNetCorr so that one could compute a weighted average for each TR rather than a straight up arithmetic mean?
-weights would cause a 1D file to be read. It would have to be as long as there are TRs in -inset
Having looked over the code briefly, I think it would yield something like RAT = (ts*w)/Nv[0] at line 41
by
Colm Connolly
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AFNI Message Board
Hey,
I updated AFNI on my mac this morning using the command below and got AFNI from Aug 28 2018. Is this build not being updated?
./@update.afni.binaries -bindir ./ -package macosx_10.7_local -no_recur
--
Thanks,
Colm
by
Colm Connolly
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AFNI Message Board
Hi Peter,
I just tried the pythonic version of the html review and like it very much. The matplotlib based graphs are so much nicer. The HTML review is a really great addition to afni.
A few suggestions:
Currently you only show the alignment of EPI and T1 in standard space. Would it be possible to show, above the standard space alignment, the alignment of the EPI and T1 in original space i
by
Colm Connolly
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AFNI Message Board
Hey,
I have some task data (only one run) from a subject that I've analyzed using afni_proc. There were three stimulus classes provided. The output of the out.ss_review.redacted.txt has me somewhat perplexed. Below, it clearly states that there were 13 TRs censored per run, but then even farther below that it says that there were 11 2 10 (=23) TRs censored per stimulus.
At most, in the
by
Colm Connolly
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AFNI Message Board
Have you thoroughly inspected the alignment of the EPI to the T1 images? Also, have you checked the brain masking?
by
Colm Connolly
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AFNI Message Board
This is the Dimon command I use. It correctly leaves the HEAD/BRIK files in the -gert_outdir. You may want to play around with the -GERT_Reco -gert_create_dataset commands and their location on the command.
Dimon -infile_pattern $sdir/'*.IMA' -dicom_org -gert_filename make.$ntask \
-save_file_list "${subject}.${ntask}.dicom.list" \
-gert_to3d_prefix "${
by
Colm Connolly
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AFNI Message Board
Thanks for the advice, Rick, much appreciated.
With respect to your pre-steady state comment, I'm using a Siemens scanner which inserts an automatically determined number of dummy scans (distacqs in GE parlance) in proportion to overall scan length, if I recall correctly) before the start of data recording proper. It's therefore unlikely that much if any pre-steady state EPI data wi
by
Colm Connolly
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AFNI Message Board
You want the AFNI_DECONFLICT variable.
AFNI_DECONFLICT=OVERWRITE will make it overwrite everything and save you the need to -overwrite.
by
Colm Connolly
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AFNI Message Board
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Pages: 12345