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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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Will do, thanks. I should note that in the conventional 3dDeconvolve (using -stim_times), I got a warning that said the analysis would assume global times, and in the *.html output, I saw the correct output (22 trials) for each event type. My assumption is that will address the varying number of trials I was getting in the -stim_times_IM case.
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Matthew Hoptman
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AFNI Message Board
Hi Rick,
I sent the files. I'll try the flag you suggest for the cases that didn't work.
Thanks,
Matt
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Matthew Hoptman
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AFNI Message Board
Hi all,
I'm trying to run a beta series analysis on some data I have. I have a task with 66 trials, 22 in each of 3 conditions (7 events per trial are modeled). I have set the trial type descriptor to -stim_times_IM for each event type, but I note that in the output, I'm seeing only 11 (but sometimes 12 or 13!) regressors per event type. I should be seeing 22, to my understanding. I
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Matthew Hoptman
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AFNI Message Board
Hi all,
I recently analyzed using an SPMG1 HRF model. I have since reanalyzed it (to deal with the left-right flip issue noted in Glen et al., (2020) and got different group-level results. I examined the output of my afni_proc.py log and noticed that in the new log, the HRF is listed as SPMG1[0] model, despite not changing the afni version. In looking at the 3dDeconvolve documentation, I not
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Matthew Hoptman
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AFNI Message Board
One other thing to note is that these are multiband images. Not sure that should make a difference, just letting you know. However, I think the EPI image may have gotten corrupted because it showed up as being in TLRC template space, which is incorrect, so I think we're probably ok, though I have no idea how the corruption occurred.
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Matthew Hoptman
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AFNI Message Board
Ugh, I had it wrong. I DID use 3dresample to reorient the images. However, as I just tested it and found that the outcome was still DO_FLIP.
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Matthew Hoptman
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AFNI Message Board
Hi all,
I recently read your article (Glen et al., 2020). I have a question based on it/check_flip.
I have images that were acquired in RPI orientation (verified with a vitamin E capsule. When I ran align_epi_anat.py, I get the outcome NO_FLIP (using the raw images as input). So far, so good.
However, previously, I had reoriented the mprage and epi images to RAI (as I know that is the afni
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Matthew Hoptman
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AFNI Message Board
Hi all,
I just wanted to check in on whether you could offer any advice on how best to do a group-level threshold on data analyzed using 3dMVM, as I do not see a ClustSim option for that program. In the past, I had seen that we could average the <3dFWHM errts*> output values across subjects to use as the smoothing parameter in 3dClustSim. Is that what one would do in the case of ACF (i.e.
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Matthew Hoptman
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AFNI Message Board
Thanks! For the conventional approach can I just average FWHMx values across subjects?
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Matthew Hoptman
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AFNI Message Board
Hi all,
I've successfully run 3dMVM on a dataset to do second level analyses. Do you have any suggestions as to what I should use to do cluster correction? I've used -clustsim in for t-tests, but that is not part of 3dMVM. I'm also not certain how to come up with a smoothing factor if that is required. I used a smoothing kernel of 4mm on my data, but I know it's the smoothnes
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Matthew Hoptman
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AFNI Message Board
Hi again,
The script seems to crash on the lines involving the :gas flag (e.g., set dset_mask = `ls ${dset_t1:gas/.nii/_mask.nii/)`. Is there a way around that? Maybe just copy the image to the _mask.nii and then set that image to dset_mask?
Thanks,
matt
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Matthew Hoptman
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AFNI Message Board
Hi again,
The script seems to crash on the lines involving the :gas flag (e.g., set dset_mask = `ls ${dset_t1:gas/.nii/_mask.nii/)`. Is there a way around that? Maybe just copy the image to the _mask.nii and then set that image to dset_mask?
Thanks,
matt
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Matthew Hoptman
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AFNI Message Board
Dear Dr. Taylor,
This is incredibly helpful. Thanks so much!
One other question that is slightly related as I am not entirely familiar with some of the AFNI lingo: If I resample an image using 3dresample, is that equivalent to regridding it? I'm asking because the FATCAT tutorial specifies a "grid" with even numbers of slices, whereas fsl's templates tend to have dimensio
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Matthew Hoptman
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AFNI Message Board
Hi all,
I am planning to use FATCAT and am preprocessing the data using fMRIPrep. The fMRIPrep by default uses the MNI152NLin2009cAsym template. Is this the same as the mni_icbm152_t1_tal_nlin_asym_09c.nii template that one can obtain online from the McDonnell BIC? I believe the 2009a version is the one that is modified in the fatcat_proc_mni_ref zip file, but I want to use the 2009c version to
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Matthew Hoptman
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AFNI Message Board
Hi all,
I am using a multiband EPI sequence with a TR of 1.4 sec, but I want to do an FIR analysis. For the "TENT(b,c,n)" function, does the width "c" have to be an integer value? The 3dDeconvolve command runs with a non-integer value for "c," but I wanted to know whether there are any rules regarding the width parameter. At present, I'm thinking of something l
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Matthew Hoptman
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AFNI Message Board
Hi all,
I ran 3dMVM.R on a dataset that had 1 between-subjects variable (4 levels) and 1 within subjects variable (2 levels). However, I inadvertently set the options -SC and -bsMVT, which I realize are not needed with two levels. In every other package I've ever used, those options would be ignored with 2 levels as they could not really be computed, and I didn't see any errors, but is
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Matthew Hoptman
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AFNI Message Board
Hi all,
I am trying to compile afni v. 19.2.24 source code on an ubuntu 16.04 system.
I copied Makefile.linux_xorg7_64 to Makefile and got:
/usr/bin/gcc -V 32 -O2 -m64 -fPIC -ffast-math -mmmx -DREAD_WRITE_64 -DLINUX2 -DXORG7 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_XTDESTROY -D__COMPILE_UNUSED_FUNCTIONS__ -c nifti/nifticdf/nifticdf.c -I. -I/usr/include -Inifti/nifti2 -Inif
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Matthew Hoptman
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AFNI Message Board
Hi all,
I am using FATCAT_matplot to try to get output graphics for a paper. The journal requested a 300 dpi output. I have set this under Heatmap PNG, but I cannot then save the heatmap. I get the error downloadPlot.html. Is this to be expected? Am I missing a python package or is this a permission issue?
I'd really like to get this high-res output, because otherwise, I will have to d
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Matthew Hoptman
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AFNI Message Board
Hi all,
I'm a little unclear about a problem I'm having with fat_mvm_prep.py. I am also not sure whether it has been superseded by fat_mat_tableize.py
In the former, I don't get all of the ROIs (I get 3 ROI pairs, but I have 8 ROIs, so in theory, I'd have 28 pairs), but I don't see any error messages. I did have to manually edit some of my *.grid files because they d
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Matthew Hoptman
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AFNI Message Board
Hi all,
I recently watched a video in which Rick Reynolds made a case to avoid filtering resting state data at short TRs because of losses of degrees of freedom. He suggested using 3dTproject to get rid of unwanted frequencies (if I understood correctly). However, wouldn't that result in a loss of degrees of freedom? My sense was it mainly served to make the issue more explicit.
If the
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Matthew Hoptman
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AFNI Message Board
Hi all,
I ran an analysis in which I specified TENT(0,15,6) for my stimuli. I see the expected subbriks in the STATS file, but I'm getting 12 subbriks in the corresponding iresp files. TR=1.4 sec. My understanding is that the number of values in iresp should correspond to the number of TENTS requested. Could you please let me know what's going on?
Thanks,
Matt
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Matthew Hoptman
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AFNI Message Board
Hi,
I'm a fan of FATCAT, but I had a question (not directly related to FATCAT). I'm using MINIP with AND logic. My understanding is that should limit tracks to only those between ROI pairs (e.g., ROI1-ROI1). However, when I look at the *.grid file and the images that are put out by the -dump_rois (e.g., NET_000_ctx-lh-lateralorbitofrontal__ctx-lh-lateralorbitofrontal.nii.gz, I notice t
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Matthew Hoptman
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AFNI Message Board
Hi Gang,
What is the consequence of using 3dDeconvolve'd data rather than REMLfit data in 3dMEMA, in terms of outcomes? Is it acceptable to use 3dDeconvolved data in such a case? What is the alternative if one only has beta images?
Thanks,
Matt
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Matthew Hoptman
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AFNI Message Board
To whom it may concern:
Could someone please tell me what the the CHI file refers to that comes out of fat_proc_dwi_to_dt? Is it useful in QC for DTI?
Thanks,
Matt
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Matthew Hoptman
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AFNI Message Board
Ugh, I don't have those, just the 1st level beta images (I didn't do the first level analyses). If it helps, we used 3dBlur_to_FWHM setting a FWHM of 8mm. Is there any alternative approach?
Thanks.
Matt Hoptman
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Matthew Hoptman
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AFNI Message Board
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