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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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Hi AFNI experts,
I am attempting to merge Examples 8 (surface) and 11 (resting-state) from the afni_proc.py help to run rs analyses on the surface, but I am getting an error. The error is here:
** -regress_anaticor: not ready for surface analysis
** script creation failure for block 'regress'
Something seems to not be merged properly in my command between the two examples.
by
kblacker
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AFNI Message Board
Hi Rick,
I followed your advice and merged Examples 8 (surface) and 11 (resting-state) to do resting-state preprocessing on the surface, but when I run my afni_proc.py command I am getting an error. The error is here:
** -regress_anaticor: not ready for surface analysis
** script creation failure for block 'regress'
Something seems to not be merged properly in my command betwe
by
kblacker
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AFNI Message Board
Hi AFNI experts,
My question is about when it is appropriate to map data to the surface for resting-state analysis. I am following example 11 from the afni_proc.py help, but I would like to know what the advantages or disadvantages are to mapping the data to the surface before the regress steps or after the regress steps. The dataset I am working with is from a patient population and I am inte
by
kblacker
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AFNI Message Board
Hi AFNI experts,
I am working on a dataset that involves retinotopic mapping and so I chose to run all of my analyses on the surface using SUMA. However, I am also interested in whole brain results beyond visual cortex and I am struggling with how to report those results in a way that can be be compared to other studies that use volumetric data analysis. My first question is: what is the best/
by
kblacker
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AFNI Message Board
Thanks very much, Ziad! These were exactly the issues I was looking to clear up.
Kara
by
kblacker
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AFNI Message Board
Hi AFNI experts,
In preparing a manuscript for a recent study, in which I used surface-based analyses...I have run into a question about how to estimate spatial smoothing to determine cluster correction. In volumetric data, I have read that it is preferable to calculate cluster correction using the calculated smoothness of individual-level residuals and then average that smoothness across par
by
kblacker
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AFNI Message Board
Thanks very much, now the results are much clearer and more obvious how to interpret. Thank you!
Kara
by
kblacker
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AFNI Message Board
Hello again,
I have some additional clarification questions about using and interpreting the results of slow_surf_clustsim.py and quick.alpha.vals.py.
I first ran:
slow_surf_clustsim.py -save_script surf.sim \
-uvar spec_file fs/SUMA/std.141.p01_lh.spec \
-uvar surf_vol p01.results/p01_SurfVol_Alnd_Exp+orig \
-uvar vol_mask p0
by
kblacker
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AFNI Message Board
Dear AFNI experts,
I am trying to interpret the results of my surface-based analyses after running group-level stats using 3dttest++. My question is about how do I determine the “Area” and “Conn” variables, based on a corrected p-value in the interactive clustering function in SUMA?
First, what I have done so far in SUMA with interactive clustering is set the threshold slider to my desired
by
kblacker
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AFNI Message Board
Hi Rick,
Thank you very much for the clear explanation of the order of align and volreg blocks and the relevance of skull stripping to surface-based analyses. As for the alignment issues, I am still having no luck.
I ran my preprocessing script with 3 different align_epi_anat.py variations which are below and I get the exact same alignment, which is poor in every case. I also thought maybe
by
kblacker
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AFNI Message Board
Dear AFNI experts,
I have 3 questions pertaining to skullstripping and epi2anat alignment prior to surface-based analyses. My afni_proc.py command and the resulting “align” and “volreg” block scripts are below.
My first two questions are more conceptual (please feel free to point me toward any user/help documentation if you think it can fully answer my question(s)):
1) why does the afni_p
by
kblacker
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AFNI Message Board
Hi Ziad,
Okay, yes you are absolutely correct about where I went astray with the standard meshes. I had used the below afni_proc.py command to create my preprocessing script and instead I should be using the second one listed below, correct? Can you please confirm that my second (new) afni_proc.py command below is appropriate? (I intentionally excluded a blur block because my study includes re
by
kblacker
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AFNI Message Board
Hi again, Ziad,
I wanted to give you a little more information about my problem with the ConvertDsets error, which may help you to answer my question. First, I tried re-running my afni_proc.py command with the regression block included, I used all of the defaults, as used in Example #8 in the help (surface-based). And I get the same error with ConvertDsets as I posted before.
Also, my reaso
by
kblacker
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AFNI Message Board
Thanks Ziad! I will try re-running my afni_proc.py with the regression included (instead of doing it separate) in the meantime. I also just posted some additional information and error messages from my problems with ConvertDsets. I'll look forward to hearing back from you later in the week.
Kara
by
kblacker
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AFNI Message Board
Nick,
Thanks for the explanation of the node index values; that was very helpful. However, when I set the pad_to_node value as you suggested I am still getting the same error message. One thing that occurred to me is that my input data for ConvertDsets was the result of my GLM for that individual subject. I tried running it on my pre-processed data, before running the GLM as well and got the s
by
kblacker
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AFNI Message Board
Nick, thanks for the info on standard meshes in SUMA. It was very helpful and clarifying.
Also, I did run into the problem you predicted using 3dttest++ because I do not have full cortex coverage in my functional data. I tried to use ConvertDsets as you suggested but I am getting an error that I can't figure out. Below is my script and the error message:
Script:
foreach subj ( p01 p02
by
kblacker
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AFNI Message Board
Hi AFNI experts,
I am doing a surface-based analysis using SUMA and I have a few questions about standard meshes. At this point, I have created surface models using FS and run @SUMA_Make_Spec_FS (which I understand from the handouts is the point at which my standard meshes are created, correct?). I have run preprocessing using afni_proc with the surf block included. I structured my afni_proc o
by
kblacker
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AFNI Message Board
Dear AFNI experts,
I am attempting to analyze retinotopic mapping data using @RetinoProc, but I only did meridian mapping, not polar angle mapping because I only need to delineate the borders between v1, v2, and v3(possibly). I looked at all of the sample scripts that came with the demo data and it looks like @Proc.CLW-CCW is most like what I want, but it still seems like this script expects p
by
kblacker
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AFNI Message Board