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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
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Is there any way to figure out exactly what function AFNI uses for its canonical HRF -- i.e., exactly what is convolved with each regressor in a typical call to 3dDeconvolve?
Thanks,
Dan
by
dbliss
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AFNI Message Board
How can I display to the screen or convert to a more easily readable format (e.g., CSV) the contents of a .1D file?
I have my realignment parameters saved in a .1D file with one row and 12 columns, and I can't figure out how to read them. I can plot them with 1dplot, but I want the precise values in an easily manipulable format.
Thanks,
Dan
by
dbliss
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AFNI Message Board
align_epi_anat.py includes a call to 3dAllineate with the option '-weight_frac 1.0'. But in the documentation for 3dAllineate, this option isn't listed. What does it mean?
Thanks,
Dan
by
dbliss
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AFNI Message Board
Hi,
I'd like to find all voxels within an ROI whose beta coefficients for a particular contrast are significant, corrected for the false discovery rate. Is this the way to do this:
3dFDR -input stats.subject'[133]' -mask roi_subject+orig -prefix sig_voxels_subject
Here, stats.subject is the stats file output by 3dDeconvolve, and 133 is the sub-brick with the beta coeffici
by
dbliss
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AFNI Message Board
Is
3dcopy fred+orig ethel.nii.gz
equivalent to
3dAFNItoNIFTI -prefix ethel fred+orig
gzip ethel.nii
?
by
dbliss
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AFNI Message Board
In order to use -xrestore I would have had to use the -xsave option in the previous run, right?
by
dbliss
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AFNI Message Board
Is there any way to test a contrast after the call to 3dDeconvolve has already been made, without re-running 3dDeconvolve? I'm looking for a command-line way of doing this, but I'll take a way to do it in the GUI -- beggars can't be choosers.
When I say "contrast," I mean what would normally be specified in the call to 3dDeconvolve using the -gltsym and -glt_label opt
by
dbliss
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AFNI Message Board
Ah, OK, now I understand. Thanks! As a note for others reading this, that e3a_only file is *not* written (or at least not present when the script finishes) when the datasets are not oblique and motion correction is not being performed. Its sudden appearance when my datasets were oblique was what was throwing me.
by
dbliss
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AFNI Message Board
Thanks so much for your help. You've resolved a huge amount of confusion and worry I had about whether I was processing my data correctly.
by
dbliss
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AFNI Message Board
I thought 8391-T1_al_mat.aff12.1D was the main result of the script. You're saying 8391-T1_al_e2a_only_mat.aff12.1D is? Then what is 8391-T1_al_mat.12.1D?
Thanks,
Dan
by
dbliss
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AFNI Message Board
Thanks very much for the explanation. Is it fair to conclude from your answer that if I run
3drefit -deoblique -xorigin cen -yorigin cen -zorigin cen 8101-T1+orig
3drefit -deoblique -xorigin cen -yorigin cen -zorigin cen 8101-EPI-01+orig
immediately after reconstructing the scans (before running 3dTshift), and if that gets rid of my alignment problems, I'm all set? That may be the s
by
dbliss
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AFNI Message Board
Hold on, sorry, there were some other differences between the processing stream that gave me good alignment, and the one that gave me bad alignment, aside from the 3drefit calls. In the "good alignment" stream, I also reoriented the EPI and anatomical to both be RPI, and I cut some slices below the brain out of the anatomical, all before running 3dTshift and align_epi_anat.
For sure
by
dbliss
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AFNI Message Board
Thanks for the replies, but there is something that's still confusing me about this obliquity issue.
When I reconstruct my anatomical and EPI scans from DICOMs with the following commands
to3d -prefix 8101-T1 8101_DICOMs/*.dcm
to3d -skip_outliers -prefix 8101-EPI-01 -time:zt 27 273 2.0s alt+z EPI01_DICOMs/*.dcm
both are oblique.
If I then try to align the anatomical scan to the
by
dbliss
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AFNI Message Board
In order to align a session's anatomical scan to the first volume in the first EPI run, I'm issuing the following command:
align_epi_anat.py -anat 8391-T1+orig -epi pb01.8391.r01.tshift+orig -epi_base 0 -volreg off -tshift off
This caused a file I wasn't expecting to be created:
8391-T1_al_e2a_only_mat.aff12.1D
I can't find any description of this file in the align
by
dbliss
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AFNI Message Board
Thanks very much! That answers all my questions completely.
by
dbliss
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AFNI Message Board
So why all the warnings? Any fMRI practitioner knows that for two scans to be aligned, you have to align them. And yet AFNI makes it seem like something's wrong with the data and extreme measures must be taken if two datasets don't start out aligned.
Also, align_epi_anat.py does not put the anatomical and EPI scans in the same orientation. If one starts out RPI and the other RAI,
by
dbliss
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AFNI Message Board
Am I the only person who thinks this is insane?! You want to reorient your EPI before preprocessing it, and when you do that, all the slice-timing information is thrown away! And that this has happened is not made obvious to the user!
Is it guaranteed that this command
3drefit -atrcopy OLD+orig TAXIS_OFFSETS -atrcopy OLD+orig TAXIS_NUMS NEWi+orig
will restore the slice-timing informati
by
dbliss
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AFNI Message Board
Hi,
I've just reconstructed AFNI files from anatomical and EPI DICOMs. AFNI is giving me a lot of fuss about the datasets being oblique. Specifically, it says,
"If you are performing spatial transformations on an oblique dataset, or viewing/combining it with volumes of differing obliquity, you should consider running:
3dWarp -deoblique
on this and other oblique datasets
by
dbliss
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AFNI Message Board
Ah, thank you! I thought the -I option applied to the matrix that followed it, not the one that preceded it. But I'm still confused, because the mat.r$run.vr.aff12.1D, which follows -I, should also be getting inverted.
I totally agree that the alignment should always be checked manually -- I just wish the workings of these commands were less opaque, so I could know ahead of time exactly w
by
dbliss
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AFNI Message Board
Unbeknownst to me, I ran my preprocessing in afni (slice-time correction, EPI/anatomy alignment, and motion correction) with the EPIs in RAI orientation and the anatomical scan in RPI orientation. Yet, the alignment between EPI and anatomy looks good when I view it in the AFNI GUI. Am I to infer that AFNI can compare datasets perfectly sensibly even when their in different orientations? Or sho
by
dbliss
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AFNI Message Board
My criticism holds even when I call the script as you recommend. I can't see why the anat2epi transformation should ever be applied to other EPI volumes.
by
dbliss
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AFNI Message Board
Fair enough, but the call to cat_matvec is described as catenating the volreg and epi2anat transformation, but it is catenating the anat2epi transformation with the volreg one.
And I don't see why the anat2epi transformation should be applied to the volumes of the EPI for which it is desired that volume registration and registration to anatomical scan be performed. What should be there i
by
dbliss
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AFNI Message Board
As a follow-up, does align_epi_anat perform alignment on skull-stripped versions of the anatomical and EPI datasets by default?
by
dbliss
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AFNI Message Board
I'm trying to perform volume registration by aligning the first volume of the first EPI run to the anatomical scan, and then every other volume from all runs to that first volume.
In my call to afni_proc.py, I'm including the options
-align_opts_aea
-epi2anat
-volreg_align_e2a
Yet, within the volreg block of the resultant proc script, the following appears:
# catenate volr
by
dbliss
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AFNI Message Board
What is the difference between the align_epi_anat.py options -save_skullstrip and -save_orig_skullstrip? In the documentation, the -save_skullstrip option is described as requesting that the non-aligned skull-stripped dataset be saved. Is this not the original one? And which dataset is being saved: the anatomical or EPI?
by
dbliss
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AFNI Message Board