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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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Many thanks, Daniel. If I understand correctly, clicking the "WamI" button seems to provide the same information as that contained in the AFNI Cluster Results window. The issue I'm struggling more with is choosing the cluster threshold and correctly identifying the regions. This paper (http://www.ncbi.nlm.nih.gov/pubmed/24412399) seems to suggest using a primary threshold that redu
by
Alain
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AFNI Message Board
Hi all,
I've been trying to decide how to identify the location of clusters of activation. For example, I have a contrast which has identified the areas in which a group of hypertensive subjects (HPTN) have shown more activation than the diabetic (DM) subjects.
My initial approach was in FSL. I had multiplied the HPTN > DM contrast with each atlas label for the Harvard-Oxford atlas
by
Alain
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AFNI Message Board
Hi all,
I'm having some issues with determining maximum motion displacement before and after censoring using 1d_tool's -show_max_displace option. For example, with one of my subjects, the maximum motion displacement value only changes after censoring if I set the Euclidean norm cut-off (-censor_motion) at 0.7 or lower. If I use 0.8 or higher, the maximum motion displacement value doe
by
Alain
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AFNI Message Board
Many thanks for the reply, Rick. I think I've managed to sort out the problem. I was working from a script provided to me by someone in my lab. The source of the issue was the censor counts, not the generated censor files.
1d_tool.py -infile out.censor.101.breathhold.E.1D -quick_censor_count 0 -show_trs_censored comma
For whatever reason, wherever the script used -quick_censor_count 0,
by
Alain
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AFNI Message Board
Hi all,
I've been using the script below to identify and censor TRs with signal and motion outliers in my data. However, I've noticed that the options reporting statistics from these censor files does not seem to match the file content. In the censor file, shouldn't there be a zero for an omitted TR and a 1 for an included TR, and these should correspond to the TRs indicated by
by
Alain
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AFNI Message Board
Thanks! When using this function, what is the most appropriate way to incorporate the breathhold delay? The literature using AFNI for breathhold analyses often uses terms like "the block regressor delayed by 9 s". Do I simply add 9 s (or whatever the chosen lag) to each stimulus onset time in the stimulus timing file, as I had done before?
by
Alain
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AFNI Message Board
Great! Would I simply replace Block(15,1) with SPMG2 in the following script?
3dDeconvolve -input 101.breathhold.BOLD.nophymotcorr.tcat.scale.nii \
-polort 2 \
-num_stimts 1 \
-stim_times 1 breathhold_stimulus.1D 'BLOCK(15,1)'
by
Alain
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AFNI Message Board
Hi all,
How would one go about convolving the block task timing for a breathhold task in 3dDeconvolve with FSL's Double-Gamma HRF with temporal derivative and temporal filtering? I'm conducting separate analyses in AFNI and FSL, and I want to ensure the models are fairly similar. Also, does AFNI's block function in 3dDeconvolve significantly differ from this?
Thanks,
Alain
by
Alain
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AFNI Message Board
That worked out great! Many thanks again for everything.
I've run into one other wrinkle. Part of what sent me on this path was that I wanted to use similar assessments of model fit for my analysis in AFNI as for my analyses in FSL, as it is the same data set. I had moved to AFNI to conduct a different piece of the analysis examining task compliance using activation in the superior sagit
by
Alain
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AFNI Message Board
Many thanks, Gang. Perhaps I am missing something obvious. For (2) the regressor against the data across all significant voxels, how would I get a plot showing the timeseries data averaged across all of the significant voxels rather than looking at one voxel at a time?
Also, I mean the fitted model against a timeseries averaged across the significant voxels, not an individual regressor within
by
Alain
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AFNI Message Board
Hi all,
I conducted an analysis of a breathhold task with 3dDeconvolve. Over the course of examining the results of this analysis, some questions have come up for me regarding whether the model is a good fit for the data. I was wondering if there is a way to assess model fit at a level higher than whether the subjects showed activation in association with the breathhold, or by checking the mod
by
Alain
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AFNI Message Board
For example, is there a way to look at model fit against the time series for the peak voxel (a graph similar to FSL's tsplot output)? Or, is there a way to go to a specific voxel, so I can compare that voxel for a subject across versions of the model (including an average delay, 9s delay, no delay, etc)?
by
Alain
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AFNI Message Board
Many thanks for the suggestions. I will look into these options.
Regardless of how I go about doing the adjustment to the regressor, do either of you have any suggestions about how to assess the model fit beyond this link from Gang's page?
If using the second suggestion from this page (modeled signal), can I assume if the peaks and valleys of the model and data line up fairly well tha
by
Alain
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AFNI Message Board
Many thanks, Gang. I think I have the scaling part sorted now.
I did have a question about adding a delay to the BH onset times. I'm wondering what sort of delay is incorporated into 3dDeconvolve's block analysis that makes it inappropriate to add a delay. It might make sense to use a built-in delay for behaviours like button pressing tasks, but I have read in the literature about sp
by
Alain
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AFNI Message Board
Perhaps I don't understand the scaling process too well. I got this script from someone else in my lab where they scaled the data to have a range of 0-200 and a mean of 100. I tried to apply the same logic to my analysis using a range of 0-1 and a mean of 0.5. I just want to scale the data in a way that allows me to interpret the beta weights in the manner you described in your initial respo
by
Alain
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AFNI Message Board
Many thanks, Gang. If I were to scale the data for this, would I set the mean as 0.5 with a range from 0-1? Perhaps with a script like the following?
## scale each voxel time series to have a mean of 0.5, subject to a range of [0,1]
3dTstat -prefix rm.mean.nii 101.breathhold.BOLD.nophymotcorr.tcat.nii
3dcalc -a 101.breathhold.BOLD.nophymotcorr.tcat.nii -b rm.mean.nii -c 101.brain_mask+or
by
Alain
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AFNI Message Board
Hi all,
I had a question regarding the interpretation of the beta weights produced by 3dDeconvolve. For my experiment, I have analyzed each subject's breathhold data in 3dDeconvolve using the following script:
3dDeconvolve -input 101.breathhold.BOLD.nophymotcorr.tcat.scale.nii \
-polort 2 \
-num_stimts 1
by
Alain
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AFNI Message Board
I went with the second option. It seems to work quite well, thanks!
by
Alain
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AFNI Message Board
Hi all,
I was wondering how to remove an ROI from a whole brain mask. I created the whole brain mask using 3dAutomask with each subject's functional data, which seemed to work pretty well. I also have another ROI I created.
To get the whole brain and ROI mean activation values, I used each mask with 3dROIstats to draw from the stats output of 3dDeconvolve. However, as I want to see how
by
Alain
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AFNI Message Board
Hi all,
If I have functional time series data for a subject saved as a .nii file, how do I create a single functional image (an average map of the time series) for that subject? I don't want any thresholds or statistical analyses applied (beyond simply averaging across the time series to create the single image).
Thanks,
Alain
by
Alain
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AFNI Message Board
I think I understand your explanation of the SNR piece of it. I'll let you know if I run into any issues.
I'm having some issues with extracting the stats from the ROI, however. Both 3dmaskave and 3dROIstats, as you know, both specify that the mask dataset and the input dataset must have the same number of voxels.
However, the ROI I have is not overlaid onto the brain in the same
by
Alain
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AFNI Message Board
Hi all,
I have an ROI from a functional scan template that I am working on aligning with each subject's functional data. I also have the stats output image from the individual-level analysis in 3dDeconvolve. Once I have aligned the ROI, I was wondering what approach I could take to quantifying activation within this ROI. Also, how do I calculate SNR for this ROI?
Thanks,
Alain
by
Alain
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AFNI Message Board
I decided to go with using align_epi_anat with lpa cost function to align the template functional image (sss_template) with my subject's functional data (201.breathhold.BOLD.nophymotcorr.tcat.nii). Both were functional images that were not skull-stripped.
align_epi_anat.py -dset1to2 -dset1 sss_template.nii.gz -dset2 201.breathhold.BOLD.nophymotcorr.tcat.nii -dset1_strip None -dset2_strip
by
Alain
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AFNI Message Board
Hi Rick,
Another issue I was wondering about was how to evaluate how well my model fits the data after I have run 3dDeconvolve. I'm more familiar with the time series plots produced by FSL's FEAT analysis, where it is as simple as seeing whether the model and data line up relatively well. I'm sure there must be a way to produce a similar graph in AFNI. I see there are the -fitts
by
Alain
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AFNI Message Board
Many thanks, Daniel. I should have also mentioned that the template is a functional scan. If I understand correctly, the options you mention seem to deal mostly with warping one anatomical to another or functional data to an anatomical template. Is there a way to warp a functional scan to another functional scan? If not, how else can I use a functional template with an ROI specified on that templ
by
Alain
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AFNI Message Board
Hi Daniel,
Many thanks for the suggestions. I'm still a bit confused by how to approach this problem. The SSS ROI I was provided with occurs in a different space than the native space for my subject. It is not an ROI from an atlas. It fits on the right area of the template image they provided me with. But how do I transform that ROI so it fits on the right area of each subject's anat
by
Alain
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AFNI Message Board
Hi all,
I have been provided with an ROI for the superior sagittal sinus, but my anatomical and functional scans are in native space. How do I convert the ROI into native space? Suggestions are very much appreciated.
Cheers,
Alain
by
Alain
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AFNI Message Board
Many thanks for the prompt reply, Rick. It seems to be working fine now.
However, in relation to setting up the regression, I still have some questions about BLOCK and GAM. I've read the help output for 3dDeconvolve for these options, but I admit I don't entirely understand them. I haven't had too much luck understanding other sources online either.
I modelled the task by:
1
by
Alain
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AFNI Message Board
Hi all,
I have BOLD data from a breathhold task that I want to analyze using 3dDeconvolve, but I'm not sure how to proceed. I will begin by providing some context for my question.
The scan length was 5 minutes and 24 seconds (including 12s of scanner warm-up. There were a total of 78 TRs, with each TR = 4s (to accomodate BOLD and ASL scanning; I'm focusing on the BOLD piece right
by
Alain
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AFNI Message Board