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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
Hi Nick,
You make a good point, this should be fixed properly. I just went over the necessary changes this with Rick and we should have something ready in the next few days. GIFTI surfaces produced by SUMA will be LPI.
cheers,
z
by
ziad
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AFNI Message Board
nick Wrote:
-------------------------------------------------------
> Hi Ziad,
>
> ziad Wrote:
> --------------------------------------------------
> -----
> > Problem solved, I hope. The gifti coordinates
> > transform was being applied after center of
> mass
> > computation. The next set of binaries will
> contain
> > the fix.
>
&g
by
ziad
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AFNI Message Board
Hi Nick,
Problem solved, I hope. The gifti coordinates transform was being applied after center of mass computation. The next set of binaries will contain the fix.
cheers,
Ziad
by
ziad
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AFNI Message Board
Hi Nick,
It does look like there is an LPI/RAI problem here but I am not sure where it is getting introduced. I do use GIFTI versions of FreeSurfer surfaces fine so there has to be something else going on here.
If I understand what is going correctly, if the GIFTI files do not have the affine transform modified to have -1 in the 1st two diagonal elements, then after pressing 't',
by
ziad
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AFNI Message Board
Hi mw,
If the physio file you have is a simple ascii table of numbers, you can easily extract its contents with 1dcat. As Daniel said, RetroTS expects the input to be a single ascii column of numbers that represents the sampled cardiac or breathing depth function. Before we discuss reformatting the input to RetroTS, you need to understand what is in your physio file. What is stored in this m x
by
ziad
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AFNI Message Board
Hi Wolfgang,
Could you send me an anonymized version of this dataset and the command you used so that I can take a closer look?
cheers,
z
by
ziad
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AFNI Message Board
Hi Ryan,
I had never noticed this because I don't have compression set on my machine. 3drefit is doing the origin shift (from the @Align_Centers command) and because - I suspect - you have AFNI_COMPRESSOR set to GZIP it is writing out a .nii.gz file even if the input is a .nii.
My impulse is to keep 3drefit from changing the compression in the first place, but I have to consider this c
by
ziad
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AFNI Message Board
Hello,
As Rick suggested, IsoSurface should do what you want.
cheers,
Ziad
by
ziad
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AFNI Message Board
You can run independent SUMA sessions but you cannot have them all taking to the same AFNI. You can run independent SUMA/AFNI/Other sessions if you give each session a separate block of ports by assigning a separate port bloc number to each session with option -npb
cheers,
z
by
ziad
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AFNI Message Board
Hi Eamon,
There are no surfaces from the TT_icbm452 but there are some for the TT_N27 brain. If all you want is to display the results on a surface, then using the surfaces is is enough. A slight improvement would be to warp to the TT_N27 template since the surfaces are created from it.
Your question about the better way to do the warping depends on what you are after in the end. If you are
by
ziad
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AFNI Message Board
Hi Oori,
In addition to Nick's suggestion, consider ROIgrow 's -insphere option, it should do what you want.
cheers,
Ziad
by
ziad
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AFNI Message Board
Hi Danny,
If your R version is too old, it would not hurt to upgrade, R is your friend.
cheers,
z
by
ziad
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AFNI Message Board
Hello Daniela,
It is hard to say what is causing FSL to display a white blob since I am not familiar with it. Can you tell what values fslview reports when click at some voxel? Perhaps some scaling value is getting ignored. Consider using: 3dcalc -datum float -a 'YOUR_DATASET.nii' -prefix YOUR_DATASET.f.nii and try again with the new float dataset.
cheers,
Ziad
by
ziad
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AFNI Message Board
Stefania Wrote:
-------------------------------------------------------
> Dear experts,
>
> I'd like to correct physiological noise in
> resting-state fMRI data using RetroTS.m,
> but I've got some doubts:
>
> First, could I use it if cardiac and respiratory
> data have different sampling rates?
Yes you could but you'll need to resample the time
by
ziad
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AFNI Message Board
Yes you need R for ExamineXmat, do you not have it? I highly recommend it as many statistical tools in AFNI depend on R.
cheers,
z
by
ziad
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AFNI Message Board
Hello Danny,
There are a couple of tools to examine your X matrix.
One is called xmat_tool.py, and one called ExamineXmat. There is a third matlab-based one called ExamineXmat.m
Try them out and see how far you can get.
cheers,
Ziad
by
ziad
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AFNI Message Board
Hello folks,
You can blame Nick for that one Iain. For datasets with largish numbers of sub-bricks the program turns to a different type of menu selection. The trigger for the switch is controlled by the environment variable: SUMA_ArrowFieldSelectorTrigger that would reside in your ~/.sumarc (update whatever you have with suma -update_env ) then change that env from its default of 200.
The
by
ziad
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AFNI Message Board
Hi John,
There isn't one at the moment. I have been wanting to rewrite the process in R but have not yet gotten around to doing so, unfortunately.
cheers,
z
by
ziad
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AFNI Message Board
Hello folks,
(Sorry for the delay, for some reason the message did not post when I wrote it a few days ago.)
As Nick said, there can be many reasons for the discrepancy and in some cases the error will depend on the shape of the ROI.
If you to measure the volume attributed to a surface patch, the best estimate is obtained with SurfPatch. Example 1 in that program's output shows how th
by
ziad
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AFNI Message Board
Hi Jie,
What you are trying to do is OK, but the problem is in the way you are turning the ROI into a 1D file. You should use ROI2dataset to transform the ROI into a dataset. Also, I would avoid the 1D format which is lossy and stick to NIML instead. 3dSurf2Vol's -sdata option supports NIML or GIFTI input.
I assume the ROI was drawn on a standard mesh surface, so if that is the case,
by
ziad
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AFNI Message Board
Hi Kyle,
The difference in the display reflects my preference for the default rendering of the surface convexity. Edit your ~/.sumarc file so that variable SUMA_ConvColorMap is not not gray02, but ngray20 (these colormap names are the same as the ones you see in the surface controller GUI).
That should bring you back to where you were before. Future suma -update_env will not modify change
by
ziad
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AFNI Message Board
Hi Colm,
Thanks for pointing the problem on line 23 I'll be taking care of it.
cheers,
z
by
ziad
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AFNI Message Board
Hello Anjali,
The annot files are created when FreeSurfer parcellates the surfaces. You seem to want to map the volumetric atlas labels onto the surface models for the N27 brain. You could do something like that with 3dVol2Surf using the N27 brains that are in the same space as the atlas (http://afni.nimh.nih.gov/pub/dist/tgz/suma_TT_N27.tgz, MNI N27).
cheers,
Ziad
by
ziad
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AFNI Message Board
Hi Jill,
We'll fix this lovely error, but we should also update the text for that link to state that these documents are now old. A recent set of documents and data can be found in suma.pdf and suma_demo.tgz.
cheers,
z
by
ziad
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AFNI Message Board
Hi Paul,
I have been itching to rewrite RetroTS but thanks to cortisone I have been able to avoid doing so. I'll consider the Jones approach if/when I rewrite. Feel free to ping me again in a month or so. Perhaps my prescription would have run out by then.
cheers,
z
by
ziad
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AFNI Message Board
> > You make the point that
> > smoothness estimation does not matter since
> you're
> > using using bootstrap methods to determine
> > significance, but the ad-hoc method will raise
> > concerns that the results will never hold up to
> > replication.
>
> Are you concerned about replicability of which
> nodes are connected to each ot
by
ziad
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AFNI Message Board
Hi Wayne,
Hard to tell what is going on but I suspect the dataset are way off compared to the template. For example, if datasets are quite oblique you can specify an initial transform to deoblique them first. Read @auto_tlrc's help for option -init_xform and see if suggestions made there help you get better results.
Otherwise, upload a sample dataset and I will try to look into what is
by
ziad
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AFNI Message Board
Hi Nick,
I can't help but think the approach is not a good idea. You list the reasons in your posting and I would add that I don't like that some parts of the resultant beast are 2-manifold and some are not. I am surprised the clustering program does not crash and burn on such objects. You make the point that smoothness estimation does not matter since you're using using bootst
by
ziad
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AFNI Message Board
Hi Justin,
auto_warp.py is a prototype that is nowhere near ready for human consumption! I can't believe you found it so quickly. Give us some time to polish it a little before you start using it. Not too long from now, I promise.
cheers,
z
by
ziad
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AFNI Message Board