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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,
>
> I have niml.dset cortical thickness files
> converted from Freesurfer.
> I want to see the atlas coordinates in SUMA.
What do you mean by seeing the atlas coordinate? Do you mean the area's name based on some atlas? If yes, then which atlas do you have in mind?
> How can I see it? Actually my niml.dset files are
> the output of 3dMVM, so I do not ha
by
ziad
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AFNI Message Board
Hi Iain,
I think I have found the problem. I will rebuild overnight so please update tomorrow, try again and let me know.
cheers
Ziad
by
ziad
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AFNI Message Board
Hmmm. I can't get it to crash. Worse, I can't even get the xorg7 to crash...
Let's try a very specific approach:
suma -i ld4 -drive_com '-com surf_cont -view_surf_cont y'
then try to set the threshold. Does that cause the crash?
If there is a crash, try this (redirection of stdout and stderr in csh syntax):
suma -trace -i ld4 -drive_com '-com surf_con
by
ziad
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AFNI Message Board
Hi Andy,
I don't seem to be able to reproduce the problem on the openmp_64 binaries so I will need more details to try and get the crash to happen. The more detail the better.
cheers
z
by
ziad
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AFNI Message Board
Hi Andy, very strange. I am trying to look into this. I was going to suggest you go with openmp_64 but that obviously failed!
Toggle how exacly, but clicking on the 'v' button by the T selector?
z
by
ziad
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AFNI Message Board
Hi,
There is something wrong with the sphere.reg surface created by FreeSurfer. You will need to check FreeSurfer's output to find out what happened.
cheers
Ziad
by
ziad
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AFNI Message Board
Hi Xixi,
You will need to load the datasets interactively via the surface controller. Take a look at the tutorial around this section:
cheers,
Ziad
by
ziad
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AFNI Message Board
Hello Francesca,
The message is a warning so the results can still be OK. However from the rest of your message it seems like there is a problem in that the regions are not showing up properly in SUMA. If that is the case, I will need a little more detail regarding how things are misaligned in SUMA. Also, you should consider going the GIFTI route, whereby you use FreeSurfer to write the annota
by
ziad
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AFNI Message Board
Hi Robin,
We can certainly help get you going, especially since you are here at NIH. It would be best if you can bring a laptop with AFNI installed already. I'll contact you by email to set the time. Should you be heading back to Europe, there will be a weeklong bootcamp in Tubigen starting on April 13th, the class is full but you can always try and contact Xin Yu to see if you can sit th
by
ziad
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AFNI Message Board
Hi Emily,
I have made some small changes recently that might have caused such grief. I am not sure if the bug you mention is one i have fixed already because I don't have your command line. The easiest is to run @update.afni.binaries -d and try again. If the problem persists, please include the command line too along with the erratum and will look into it.
cheers,
z
by
ziad
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AFNI Message Board
Hello Mahshid,
What does afni -version return?
If your version is up to date, I will try to reproduce the problem with my sample data, otherwise I might need you to send me enough data to reproduce the error on my machine.
cheers
ZIad
by
ziad
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AFNI Message Board
Hi Pascale,
Flipping of the colormap in SUMA can be done with the 'f' key when the cursor is over the colormap. See this link for details.
cheers
Ziad
Pascale Wrote:
-------------------------------------------------------
> Hello!
>
> I have a rather basic question...
>
> I am trying to use the green monochrome map to
> display activations in both th
by
ziad
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AFNI Message Board
The answer is yes and no.
The single subject instacorr interface in SUMA does not have any of these new features. This means that you don't have access to these options if you want to do the correlations with time series defined over surfaces.
However, you could display the results of AFNI's single-subject instacorr on surface models (interactively of course) and you can set th
by
ziad
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AFNI Message Board
Hi Tie-Qiang,
I would say yes, but I am not sure what you want exactly. Here is a toy case, assuming you have installed the MNI surfaces per the new new new! instructions.
suma -spec MNI_N27:ld20
#Keyboard strokes follow
'ctrl+n' (to open a new viewer)
'[' (to hide the left hemi in one viewer)
']' (to hide the right hemi in the second viewer)
Links:
by
ziad
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AFNI Message Board
Hi Kara,
>
> Does the same rule apply with surface-based data?
Yes.
> I used a target FWHM of 4mm during my
> preprocessing. I then ran individual level GLMs
> using 3dDeconvolve and a group analysis using
> 3dttest++. Then to determine my cluster threshold,
> given my uncorrected and corrected p-values of
> interest, I ran slow_surf_clustsim.py. It sets
by
ziad
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AFNI Message Board
Hello Alicia,
Assuming you started off with a volume of zeros when drawing your ROI mask, then the only non-zero values should be where you drew your ROI. When you use such a volume as a mask, only non-zero voxels are considered. If all you have is the hippocampus then you would be using a smaller region than with the whole brain mask. Perhaps you are puzzled by the size of the mask dataset o
by
ziad
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AFNI Message Board
Hello Dustin,
You have to be careful with the scaling, very low means can put extremes in the data and those can cause precision problems in the output datasets. The best way to get a feel for our prefered processing order is to look at the output scripts of afni_proc.py. There are numerous pesky problems that you have to watch for, so if you are writing your own processing pipeline you should
by
ziad
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AFNI Message Board
Hello folks,
After much delay, there is new documentation for AFNI - well SUMA and FATCAT mostly for now at this link: http://afni.nimh.nih.gov/pub/dist/doc/htmldoc/
Feedback and corrections welcome.
Of note are the quick tours for surface, tract, and graph viewing, and Paul's FATCAT notes.
Much of this help is generated automatically by the programs themselves so I hope that th
by
ziad
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AFNI Message Board
Hello,
Use 3dUndump for that. You will need a master dataset, which can be the volume from which these corrdinates were derived, or the volume from which you want to extract the data.
Either way, the first step is to open AFNI with the dataset you will be providing as -master, and using jump to XYZ with one of the coordinates to see if you go to the correct location. I have a suspicion that
by
ziad
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AFNI Message Board
Hi Kelly,
The Zilles CA atlas information is all in volume space. Those atlases are typically installed in the abin directory (try this command if you can't find them: apsearch -list_all_afni_dsets).
In terms of using the CA defined regions as ROIs, you could map them onto the MNI_N27 cortical surface of the same standard mesh density that you're using for your other subjects.
by
ziad
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AFNI Message Board
Hi Emily,
I would recommend you use the omask option, along with specifying which MNI atlas you want to use (-atlas). Aside from the help for whereami, see examples in this pdf, page 34 in particular.
For the omask option to work, you will need to have the atlas volume on disk in MNI space. AFNI does on the fly space conversions for whereami, but not for the -omask option. So if you don
by
ziad
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AFNI Message Board
Hi Sam,
As you mentioned, you can't mix opacities between background and foreground planes. Colors from each of the two stacks are mixed separately then the resultant foreground is attenuated by the average intensity of the resultant background.
However this might work for what you want:
1- Make a convexity dataset on the command line: SurfaceMetrics -conv on the smoothwm surface (t
by
ziad
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AFNI Message Board
Hi James,
Can you send me a copy of the trouble dataset? If you need upload instructions send me an email and I will forward them to you.
cheers
ziad
by
ziad
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AFNI Message Board
Program 3dZcutup should do the trick. The -help output of the program shows how to split and reassemble a dataset.
cheers
Ziad
by
ziad
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AFNI Message Board
Hi David,
I am assuming having each bundle colored differently is not enough, is it?
If you only want bundles that touch certain ROIs, I can imagine having a masking feature where you enter a bunch of ROI labels and only bundles touching these labels woll get displayed. Is this what you have in mind? There is no such thing at the moment and it can go on the todo list. How badly do you need
by
ziad
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AFNI Message Board
(Reply also contains the answer to your email query: "I also want to know the basic algorithm behind "3dSkullStrip" as in AFNI's original paper I did not find it in a clear way. ")
All I have as written description is in the first few lines of the -help output. You need to be a lot more specific about your question regarding "Performing noise removal". There
by
ziad
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AFNI Message Board
Hi Phil,
I tried to run the test data with a TR of 1.5 instead or 2.0 and adjusting Tpol to 24, but I do not get the errors you mentioned with a similar 3dRetinoPhase command. I seem to get decent results.
Could you send all the data I need to run the 3dRetinoPhase command you mentioned in the first posting?
cheers
z
by
ziad
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AFNI Message Board
Hi Adam,
I suspect you are trying to estimate the smoothness of the noise from a dataset that has just one value in it.
What does 3dinfo -prefix -nt produce when run on the varied datasets you used in the command? Particularly the blur master?
cheers
z
by
ziad
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AFNI Message Board