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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
Sorry Phil, I kept forgetting about it. Will get back to you soon.
cheers,
z
by
ziad
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AFNI Message Board
Hello Gunjan,
What do you mean by not having the BRIK extension. Can you show me the output of:
ls PPP*
Also, what does the following command give:
3dinfo -min -max a.nii
give you?
Is this a normal T1 volume or was is preprocessed.
And lastly, you really should not be running anything from ~/abin
You should set your path to point to ~/abin and run your commands from t
by
ziad
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AFNI Message Board
Hi Cesar,
Sorry I missed the posting until Rick put it in my face! Yes the -r is meant to have the program try multiple initializations, and the -seed option is there to allow you to control the random number generator if you want to get the same results to be reproduced, given same machine, libraries, etc.
cheers
z
by
ziad
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AFNI Message Board
Helo Kickan,
This is inferred from the sform or qform of the NIFTI dataset. If you want the details, check out function nifti_mat44_to_orientation() in nifti1_io.c
cheers
z
by
ziad
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AFNI Message Board
Hello YingYang,
It looks like you're still missing your X11 fonts or some of them. Try something to the effect of:
yum install xorg-x11-fonts-misc
cheers,
z
by
ziad
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AFNI Message Board
Hello Alain,
Sorry for the delay. What you can do is convert each of the surfaces to .1D format with ConvertSurface, then use 3dMean to average the coords. Here is an example that does this for just two surfaces, the pial and smoothwm surfaces. You can do this for any set of surfaces at hand, as long as they are isotopic of course. This means you can do this on any set of standard meshes with
by
ziad
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AFNI Message Board
Hello Alain,
Your SUMA is quite old so odds are the bug has been fixed already. Please update and try again and we'll take it from there.
Update should be a breeze with @update.afni.binaries -d
cheers
z
by
ziad
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AFNI Message Board
Hi Cota,
Send me a copy of the volume in question and I'll take a look.
cheers
Ziad
by
ziad
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AFNI Message Board
Hi Seul,
I don't know about how the threshold works in the FSL viewer, but you could threshold the volume for good before passing it to FSL with 3dcalc with the step function.
3dcalc -a CORR_DSET -b CORR_DSET'' -expr 'step(b-THR)*a' -prefix BRUTE_THRESHOLD
where THRESHOLD_LABEL is the label of the sub-brick with which you are thresholding in AFNI, and THR is the
by
ziad
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AFNI Message Board
Hi Linda,
I am not sure what distance you are trying to measure, but perhaps this would help.
Say you have a location identified on a subject's surface in SUMA. You can click on that location and note the coordinate, then you can use Vecwarp to transform each coordinate to TLRC space.
All of this assumes that you are using the proper -sv volume for each subject. This can easily be ch
by
ziad
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AFNI Message Board
OK, no image was attached, try this link instead. Perhaps this http://afni.nimh.nih.gov/sscc/staff/ziad/Misc_Download/tmp/directions.jpg]one would do too.
cheers,
z
by
ziad
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AFNI Message Board
Hi David,
B. Can be done in SUMA by creating a 'Displayable Object' (DO) that is a bunch of directions. I made some code changes that allow for this to be done in the manner shown below. Commands are in tcsh syntax and to be run from the FATCAT_DEMO/DTI directory. See @Install_FATCAT_DEMO for details if you don't have it already.
cd FATCAT_DEMO/DTI
echo '#directions
by
ziad
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AFNI Message Board
Hello Ping,
You could merge the two datasets but given that 3dMVM is univariate (voxelwise), you won't get different results by combining the two hemispheres, except for FDR corrections. Nonetheless, you can still combine the two with something of this sort:
1- use FreeSurfer's mris_convert to write out the datasets in gifti format (.gii)
2- use ConvertDset to write out the two v
by
ziad
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AFNI Message Board
Hi All,
I would like to know how to merge the Freesurfer two hemisphereic surface thickness files, e.g lh.thickness.fsaverage.mgh and rh.thickness.fsaverage.mgh, into one file that 3dMVM can use. Since I have other whole brain volumetric files that are included as dependable variables, I would think it is reasonable to combine the thickness into one file. Or I have to run lh, rh separately?
by
ziad
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AFNI Message Board
Hi Mike,
Hard to tell. We do use 3dSkullStrip on T2 human data and it is OK for that, usually. For a rat T2, I can't tell and I can't tell if the absence of a spatial transform is the cause of the problem without more info. If the T2 volume looks OK in AFNI then the transform is not the problem. Have you tried to use the -visual option in 3dSkullStrip to determine what might be going
by
ziad
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AFNI Message Board
tobiamj Wrote:
-------------------------------------------------------
> Dear Ziad and Afni Experts,
>
> I'm trying to compare cortical thickness for the
> affected hemisphere of a patient group to their
> unaffected hemisphere (the affected hemisphere is
> sometimes left and sometimes right, so it requires
> surface node/vertex symmetery). Is it possible to
&
by
ziad
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AFNI Message Board
Hello Tim,
I am not sure what you mean by using fsaverage to normalize the T1mprage files, but perhaps this point is irrelevant anyway. What you should use for surf_A is an anatomically correct surface on which the dataset is defined. In all likelihood, that would be the pial surface of the hemisphere corresponding to the statistical dataset in hand.
cheers,
Ziad
by
ziad
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AFNI Message Board
Hello Tara,
It is not quite clear to me what you mean by taking the FreeSurfer mask to AFNI/SUMA.
I think the first thing you want to do is map that region to standard mesh surfaces. To do so, you will need to run on the fsaverage directory in FreeSurfer:
@SUMA_Make_Spec_FS -sid fsaverage -GIFTI
This will create a SUMA directory with fsaverage surfaces in orignal and standard-mesh form
by
ziad
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AFNI Message Board
Hola Cesar,
It is best you do the extraction using the ROI string labels directly. For example:
#Getting data from ROIs defined in the annotation files
set zone1 = G_cuneus
set zone2 = G_occipital_middle
3dcalc -a ../SurfData/SUMA/std.lh.aparc.a2005s.annot.niml.dset"<$zone1>" \
-b ../SurfData/SUMA/std.lh.aparc.a2005s.annot.niml.dset"<$zone2>" \
by
ziad
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AFNI Message Board
Hi Emily,
I don't know how aware you are of FATCAT, the library of tools that Paul Taylor developed for functional and anatomical connectivity analysis. The tools he mentioned should be in your distribution already unless your version is old (Update with: @update.afni.binaries -d).
For some data, demo scripts, and sample results, run ./@Install_FATCAT_DEMO .
cheers,
Ziad
by
ziad
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AFNI Message Board
Hi Linda,
Consider the program waver, which takes stimulus timing information and generates expected BOLD response time series. For 3ddelay, I recommend you offset your stimulus timing by about 2 or 4 seconds to be sure all FMRI responses are delayed relative to your reference time series.
cheers,
Ziad
by
ziad
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AFNI Message Board
Hello Zhihao,
The program catenates all the input to create a feature vector for each voxel. What that feature vector is depends on what you have in F1, F2, etc. The catenation of the input is simply a convenience feature, if your feature vector is already in one dataset (a time series perhaps) then you will have just that one dataset as input.
cheers,
Ziad
by
ziad
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AFNI Message Board
Hi Adam,
This is very strange. I don't know what to make of it. Is it possible at all to run this command from the console of the server? Can it be that your ssh connection is timing out? Any chance you can copy the FreeSurfer output somewhere local and run the script anew?
cheers,
z
by
ziad
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AFNI Message Board
Hi Adam,
Long time no hear. I think you have guessed the problem correctly. Can you try running the newer version:
@SUMA_Make_Spec_FS -sid MusicCog_AER -debug 2 -GIFTI ?
cheers,
z
by
ziad
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AFNI Message Board
Hello Nilufar,
Nilufar Wrote:
-------------------------------------------------------
> Hi Afni experts,
> I have a question, It would be appreciated if you
> could help me.
> I have transfered volumetric data to surface data
> using 3dVol2Surf,
So at this stage you would have created a surface-based dataset which must be loaded into SUMA with the 'Load Dset' b
by
ziad
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AFNI Message Board
PeterKohler Wrote:
-------------------------------------------------------
> 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 d
by
ziad
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AFNI Message Board
Posted on behalf of Dr. Peter Bandettini:
The National Institute of Mental Health (NIMH) invites applications for a post-doctoral position in the Section on Functional Imaging Methods, directed by Dr. Peter A. Bandettini. Our research is focused on better understanding and advancing both resting-state and activation-based fMRI. Two secondary goals are: to advance fMRI so that it can be used to
by
ziad
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AFNI Message Board
Hi Justin,
Just rename it to something else, and for when you want to load it, specify it directly on the command line with option -layout
cheers,
z
by
ziad
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AFNI Message Board
Posted on behalf of Dr. Judy Rapaport:
The Child Psychiatry Branch at the NIMH is recruiting applicants for a Staff Scientist position. Applicants should have a strong background in statistics (PhD level) and programming/computer science, as well as interests and experience in neuroimaging and behavioral research. The recruit should be adept at writing his/her own code to clean, organize, ana
by
ziad
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AFNI Message Board
Hi Taka,
Assuming you know how to form the ROIs and extract time series from these ROIs. (If you don't, read this doc). You can use the program 3dTcorr1D to perform whole brain correlations with 1 or multiple time series.
cheers
Ziad
by
ziad
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AFNI Message Board