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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
Nicreap-
I just want to make sure I'm reading this correctly. When you ran align_epi_anat.py on the original data, there was good alignment, but you saw artifacts around the Ventricles? And when you deoblique first and then run align_epi_anat.py you get a cutoff and bad alignment?
I suspect the problem with the second (deoblique and then alignment) is that align_epi_anat.py does de
by
Peter Molfese
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AFNI Message Board
Not sure if this fully answers your question, but if you use the -allineate option in 3dQwarp, you do not need to then concatenate the affine and nonlinear warps. A simple inversion should work.
From the help:
** PLEASE NOTE that if you use the '-allineate' option in 3dQwarp, to **
** do the 3dAllineate step inside 3dQwarp, then you do NOT catenate **
** the af
by
Peter Molfese
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AFNI Message Board
Hi Lz,
The names come from the Freesurfer segmentation. Our Neuroradiologist has also suggested some changes in the names, though we have not yet finalized what those alternatives might be.
We are working on the paper right now. For now, I suggest you cite:
Molfese, P. J., Glen, D., Mesite, L., Pugh, K., et al. (In Prep.)
This may add more authors to the list soon! Keep your eyes o
by
Peter Molfese
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AFNI Message Board
That's odd. Can you give us your complete command lines for align_epi_anat.py? Possibly both your first attempt and your second (with the 3dWarp step beforehand).
by
Peter Molfese
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AFNI Message Board
I have a sneaking suspicion, but let's try this. What's the output of:
afni_system_check.py -check_all
by
Peter Molfese
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AFNI Message Board
My guess is that that particular volume doesn't have enough TRs... What's the output of:
3dinfo -prefix -nt Sub0043_Ses1/bold/002/Sub0043_Ses1_bld002_rest.nii.gz
by
Peter Molfese
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AFNI Message Board
Hi Emily,
I suspect the error you're getting is because you have the first line of 0 0 0 in your bvec file. 3dDWItoDT assumes that this line exists and you can just remove it (or use row selectors) and run the program again.
You can use 3dTcat to create a new dataset without the b0 volumes or to append that averaged b0 volume to the front or both at the same time using something lik
by
Peter Molfese
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AFNI Message Board
I would try adding a pause between the launching of AFNI and the driver. You can do this in bash using the sleep() function, where sleep 2 would make it pause for 2 seconds. I think I use a value of 5 in my scripts.
Another thing you could do is have AFNI cycle through every combination that you want to view and save a picture of each, then you can quickly look through the pictures.
by
Peter Molfese
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AFNI Message Board
Hi Bridget,
I would recommend using align_epi_anat.py to do the EPI to anat and EPI to standard space transform. You can use syntax similar to the example:
@auto_tlrc -base ~/abin/TT_N27+tlrc -input sb23_mpra+orig
align_epi_anat.py -anat sb23_mpra+orig -epi epi_r03+orig \
-epi_base 6 -child_epi epi_r??+orig.HEAD \
-epi2anat -suffix _al -tlrc_apar sb23_m
by
Peter Molfese
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AFNI Message Board
A couple more questions:
1) Is there any consistent artifact or feature in the anatomicals that aren't ending up aligned? Perhaps remnants of skull from a bad skull-strip?
2) Are you aligning your EPI to anatomical using align_epi_anat.py?
3) Have you tried using 3dUnifize to adjust for any odd shading artifacts?
by
Peter Molfese
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AFNI Message Board
Hi Bridget,
You should be using Usage 1 (see help) for transforming your structural data to standard space and then Usage 2 to apply the same transform (created in in Usage 1) to your functional data. So a standard pipeline might look like this:
#transform anatomical, assumes anatomical has skull on, otherwise add -no_ss
@auto_tlrc -base TT_N27+tlrc -input Subj_Anatomical+orig -init_xfo
by
Peter Molfese
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AFNI Message Board
Try adding .niml.dset to the end of the -prefix name (i.e. filled.common.groupMEMASurf.$hemi.niml.dset). The same solution works for 3dMVM.
by
Peter Molfese
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AFNI Message Board
If you wanted to do multiple sessions within the same Xvfb instance, you can do something like:
`which Xvfb` :1 -screen 0 1024x768x24 &
export AFNI_DETACH=NO
parentDir=`pwd`
mkdir snapshots
for aSubject in Subject01 Subject02 Subject03
do
cd $aSubject/$aSubject.results
centerC=`3dCM anat_final.${aSubject}+tlrc`; #get center of anatomical
DISPLAY=:1 afni -com "OPEN_W
by
Peter Molfese
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AFNI Message Board
Are you in the directory where a.nii exists? What is the output of:
ls
and:
3dinfo a.nii
by
Peter Molfese
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AFNI Message Board
Hi Emily,
Depending on if you resampled the data in your afni_proc.py and included a "-regress_est_blur_errts" flag, then 3dFWHMx should already have run and produced a blur_est.SubjectID.1D and a blur.errts.1D inside the results folder for each subject. The first file should have the mean blur calculated and the second will have the blur estimates for each run listed out.
To m
by
Peter Molfese
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AFNI Message Board
This can be accomplished in a few different orders, one possibility is to start by creating a mask of the brain with 3dSkullStrip:
3dSkullStrip -input inputVolume.nii -prefix ss_mask.nii -mask_vol
and then multiply the mask with the original to get the skull-stripped brain (3dcalc):
3dcalc -a inputVolume.nii -b ss_mask.nii -expr 'a*step(b)' -prefix ss_volume.nii
by
Peter Molfese
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AFNI Message Board
Then you have the bash shell setup and should use the second syntax:
export PATH=$PATH:/path/to/afni/folder
by
Peter Molfese
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AFNI Message Board
It sounds like you don't have AFNI in your path. First check which shell you are using:
echo $SHELL
Then you can temporarily set your path to include AFNI by running a command such as:
tcsh:
set path = ( $path /path/to/afni/folder )' >> .cshrc
bash:
export PATH=$PATH:/path/to/afni/folder
More complete instructions here.
by
Peter Molfese
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AFNI Message Board
It sounds like you may not have AFNI in your path. Did you install using the download from the website or did you use NeuroDebian repository?
What's the output of: afni_system_check.py -check_all
by
Peter Molfese
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AFNI Message Board
3drefit will only change the header. Use this option if you think the header is incorrect.
If you want to change the header and rearrange the data, use 3dresample.
by
Peter Molfese
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AFNI Message Board
As a longshot, try naming your output file (-prefix) with the suffix ".niml.dset"
by
Peter Molfese
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AFNI Message Board
Two things to check:
1) Install all of the dependencies (afex, phia, snow)
2) It looks like each subject is contributing 5 data files to the model, but your model specification doesn't include a repeated measure (wsVars).
Your Current Model:
3dMVM -prefix test -jobs 8 -model "group+gender+age" -qVars "age"
You will need to annotate the repeated measure in the
by
Peter Molfese
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AFNI Message Board
I suspect that Debian or Ubuntu would work well in any laboratory. In addition to easy installation and configurations, many people speak highly of the NeuroDebian repository that can be useful for simple installations of different packages.
I've had AFNI (and Freesurfer, etc) running on Debian, Ubuntu, and CentOS for quite some time. Hardware support is pretty decent across most dist
by
Peter Molfese
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AFNI Message Board
If you just upgraded, then you will need to reinstall Xquartz. If that doesn't fix it for you, let us know the output of:
afni_system_check.py -check_all
by
Peter Molfese
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AFNI Message Board
The error occurs because the number of parameters you are trying to estimate is more than the number of data points available. Perhaps you can tell us a bit more about your experiment and your eventual goal in analysis.
This question has come up before, see this thread.
by
Peter Molfese
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AFNI Message Board
Can you post your 3dDeconvolve script?
What basis function are you using?
by
Peter Molfese
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AFNI Message Board
You can use -stim_times_IM from the 3dDeconvolve Help to have each event modeled separately.
[-stim_times_IM k tname Rmodel]
Similar, but each separate time in 'tname' will get a separate
regressor; 'IM' means 'Individually Modulated' -- that is, each
event will get its own amplitude estimated. Pr
by
Peter Molfese
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AFNI Message Board
Hi,
I would start with 3dSkullStrip with default options:
3dSkullStrip -input MyInput.nii -prefix MyOutput.nii
by
Peter Molfese
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AFNI Message Board
Hi Ajay-
Not to derail the obliquity thread. But perhaps you could tell us what the desired end result is. Are you wanting to map the EPIs to the surfaces or just use the segmentations? There are a couple of scripts that will handle the alignment of the Freesurfer and functional files. For example the @SUMA_Make_Spec script and @SUMA_AlignToExperiment.
P
by
Peter Molfese
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AFNI Message Board