Show all posts by user
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
Page 1 of 1 Pages: 1
Results 1 - 28 of 28
I did not mean to make light of the undertaking.
I was just trying to gauge whether I should wait for an update of 3dClustSim or take some alternative strategy. It sounds like the latter is the case. What do the AFNI gurus recommend? Should I use slow_surf_clustsim.py?
by
PeterKohler
-
AFNI Message Board
Okay.
Is that something you plan on fixing within the next couple of weeks, or would you recommend I take some alternative strategy?
by
PeterKohler
-
AFNI Message Board
Since this is a whole-brain analysis on surface data, how do you propose that I generate such a mask?
To me it looks like the -Clustsim option is not compatible with surface data, because it seems that the permutation files (TT.z9WstU9Zw8p.???.nii) should be .niml.dset, rather than .nii.
This is definitely not because I am deleting anything, it fails everytime I run it, and works everytim
by
PeterKohler
-
AFNI Message Board
I'm not using -resid. Here's an example of an exact command I run:
3dttest++ -setA 'Positive>Word' \
sub0 '/Volumes/NLine_Peter/Sizes/s2003/rh.std.141.TaskContrast.4fwhm.niml.dset[1]' \
sub1 '/Volumes/NLine_Peter/Sizes/s2004/rh.std.141.TaskContrast.4fwhm.niml.dset[1]' \
sub2 '/Volumes/NLine_Peter/Sizes/s2005/rh.std.141.TaskContrast.4fwhm.niml.
by
PeterKohler
-
AFNI Message Board
Hi Bob,
Has there been any progress on this? I am doing a one-sample t-test on surface data, and get this error when I add '-clustsim' to 3dttest++:
*+ WARNING: -setA: group label 'TT.xnSwVGJ4TIg.resid.nii' looks like a dataset name but isn't -- is this OK ?!?
** FATAL ERROR: Option -setA (long form): need at least 2 datasets
The code runs fine without -clustsim, w
by
PeterKohler
-
AFNI Message Board
None of these two options give me quite what I want, I think.
Using the mean from before detrending generates a datasets with lots of values that are zero, or near zero, which doesn't seem desirable.
Detrending after scaling generates a dataset with a range from -160 to 200 approximately, and not 0, 200, as is usually the goal of the scaling operation.
Any other ideas? I am surpr
by
PeterKohler
-
AFNI Message Board
Hello AFNI gurus,
I have a few datasets that I am doing non-GLM analyses on, which means that I would like to detrend the data, like so:
3dDetrend -prefix ${INPUTFILE}.vr.dt.nii.gz -polort 2 \
-vector motparam.${INPUTFILE}.1D ${INPUTFILE}.vr.nii.gz
The detrending works great, but I run into problems with the next step, when I try to scale the data to AFNIPROC-style, to convert values t
by
PeterKohler
-
AFNI Message Board
How would you run this for a group analysis, exactly? Which input files would you use?
by
PeterKohler
-
AFNI Message Board
Thanks so much for getting back to me.
1) Okay, that makes sense. I am able to map stats from different subjects onto the same surface, so I think this part worked fine.
2) The -oop option is indeed being applied to 3dVol2Surf in my afni_proc.py exe script.
3) So, when I run slow_surf_clustsim.py I can use the SurfVol and spec files from any one of my subjects, and the results will be
by
PeterKohler
-
AFNI Message Board
I have just started experimenting with surface-based group analysis in AFNI/SUMA, and I would like some more specific help here. I have used afni_proc.py with the options
-surf_anat ${SUBJ}_SurfVol+orig
-surf_spec std.141.${SUBJ}_?h
to do a surface-based analysis on standard surfaces for each of my subjects. My questions are the following:
1) My assumption is that I can now run 3dttest++
by
PeterKohler
-
AFNI Message Board
Hi Ziad,
thanks for getting back to me. The ROI generation is probably something I look into only if a situation arises where I really need it.
I still don't understand why the version of SurfVol that has been aligned to my epis, seems to be aligned with the surfaces, despite the fact that it is not aligned with the original SurfVol. I have now seen this with lots of datasets in diffe
by
PeterKohler
-
AFNI Message Board
Hi Ziad,
thanks for getting back to me. The reasoning behind my ROI query was that we load functionally-defined, bonified SUMA ROIs into Matlab as part of our EEG source localization pipeline. We recently started using a separate set of anatomically defined ROIs, that are defined not as bonafide SUMA ROIs, but as niml.dset file where the vertices belonging to each ROI are assigned different in
by
PeterKohler
-
AFNI Message Board
Hello AFNI Gurus
Oddly specific enquiry: Is it possible to create a surface ROI (e.g. lh.xxx.niml.roi) from a surface dataset (e.g. lh.data.niml.dset) the same way you would use 3dcalc to generate a binary mask in volume space? In other words, is it possible to generate a surface ROI automatically, instead of drawing it, or somehow convert a surface dataset to an ROI? I understand that I can u
by
PeterKohler
-
AFNI Message Board
Thanks Nick, I think I got it now. And after mucking about with my code a little I can even get results that look reasonable. I truly appreciate your help.
by
PeterKohler
-
AFNI Message Board
nick Wrote:
-------------------------------------------------------
> I don't understand this question.
> freesurfer_read_surf returns vertices and face
> indices of a surface, which is not much related to
> ROI work. Except of course that the indices in an
> ROI refer to surface vertices.
My question is really what the correspondence is between the SUMA ROI indices a
by
PeterKohler
-
AFNI Message Board
nick Wrote:
-------------------------------------------------------
> So if you read a single ROI with
> afni_niml_readsimpleroi, take all unique indices
> together present in .edge and .region, and
> subtract one from each of these, then you should
> get the same indices as the first column in
> Read_1D.
And I do. Thanks a lot for explaining the difference between t
by
PeterKohler
-
AFNI Message Board
Hello AFNI Gurus,
I am trying to use Matlab to determine which vertices of a Freesurfer surface are included in a few surface ROIs that I have created in SUMA. I load the Freesurfer surface into Matlab like this:FSv = freesurfer_read_surf('lh.pial');
I have tried two different approaches for getting the ROIs into Matlab. The first is to save the ROIs as a niml file, and loading it in
by
PeterKohler
-
AFNI Message Board
Rick? Daniel? Did you see the message below?
PeterKohler Wrote:
-------------------------------------------------------
> @Rick: I've tried with a zpad of 500, the largest
> my machine would allow, but I still have the same
> issue, in this case that the superior part of an
> epi that was originally centered "below" the
> structural dataset, is cut off in t
by
PeterKohler
-
AFNI Message Board
@Rick: I've tried with a zpad of 500, the largest my machine would allow, but I still have the same issue, in this case that the superior part of an epi that was originally centered "below" the structural dataset, is cut off in the output. Perhaps I should mention that in this case, and in fact in most cases, rotation is actually not necessary for alignment, so I only do translatio
by
PeterKohler
-
AFNI Message Board
Hello AFNI gurus,
I have multiple oblique, partial coverage EPI datasets, that I am trying to align to a structural dataset, something that align_epi_anat.py has a very hard time doing, even with various options turned on, as suggested elsewhere on this message board. I find that doing an initial alignment of the EPI dataset using the nudge plugin in Define Datamode, usually makes align_epi_an
by
PeterKohler
-
AFNI Message Board
Simple ("quick") question: How do I turn off absolute thresholding in DriveSuma? That is, the 'ITI' option in the SUMA surface controller.
Thanks!
/Peter Kohler
by
PeterKohler
-
AFNI Message Board
Thanks for the run-down, Nick. I think niml is my preferred format for surface data, but I also mostly stay within AFNI-SUMA.
by
PeterKohler
-
AFNI Message Board
... and I realize now that I can. Are .gii, .1D and .niml.dset files essentially equivalent, as far as SUMA is concerned?
by
PeterKohler
-
AFNI Message Board
Yeah, well I was confused about this too, but I think it is in fact surface data, despite the .mgh suffix. I base that mainly on the fact that I can open the .mgh file as an overlay in tksurfer, but not in tkmedit. I also tried Nick's method of converting to NIFTI using mri_convert, but was unable to produce a NIFTI file that AFNI could open. I did manage to produce a .1D file that I could v
by
PeterKohler
-
AFNI Message Board
Dear AFNI gurus,
Surely I must be missing something, but I cannot figure out how to convert a .mgh file containing FreeSurfer surface overlay data into a niml.dset file that SUMA can read.
Best,
Peter
by
PeterKohler
-
AFNI Message Board