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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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Results 1 - 30 of 405
Hi Marina,
If you ran the exact command you posted, try removing: " #we eroded the wm ourselves." from "-anat_follower_ROI WM epi wm_eroded+orig \ #we eroded the wm ourselves.", and make sure there are no characters left (not even spaces) after the '\' at the end of the line. In other words, the line with that option should read: "-anat_follower_ROI WM epi
by
ziad
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AFNI Message Board
I have a feeling you have never encountered the surface controller before...
Take a look at this overview.
cheers
Ziad
by
ziad
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AFNI Message Board
And in suma you just press 'r' right over the colorbar. Use the WHelp feature on the colormap or just see here and here for more info.
cheers
z
by
ziad
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AFNI Message Board
Hi Xixi,
If you don't want the convexity to be higlighted in the composite view, just toggle it with 'Background Attenuation' , or by hiding the background .
cheers
z
by
ziad
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AFNI Message Board
Hi Xixi,
Try having FreeSurfer a GIFTI version of the modified annotation file, then load it with SUMA. You should be able to perform the conversion with:
mris_convert -c lh.aparc_parula.a2009s.annot lh.aparc_parula.a2009s.annot.gii
then load the .gii dataset with SUMA much like you were trying with the ill fated output of FSread_annot.
Let me know if that does the trick and if not,
by
ziad
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AFNI Message Board
Hello Sabine,
SurfExtrema cannot read native FreeSurfer formats. Try converting the input to NIFTI (volumes) and GIFTI (surfaces and surface-based datasets) and the program should work fine. I am surprised running the command as you did has not produced error messages.
Cheers
Ziad
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ziad
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AFNI Message Board
Hello Matilde,
You could KIND OF do it if you mapped data onto standard meshes and used 3dGroupInCorr on the surface. Though hidden from view, the generation of standard meshes does involve non-registration of sphereical representations of the cortex, however the process is data independent so you can map single subject data onto their standard-mesh surface in original space then proceed with
by
ziad
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AFNI Message Board
Would IsoSurface do the trick for you?
IsoSurface -input brain.nii -o_gii brain.isosurf.gii -isocmask '-a brain.nii -expr(step(a)'
See IsoSurface -help for details.
cheers
z
by
ziad
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AFNI Message Board
Hi Francesca,
That's not your fault. 3dmaskdump does not know how to handle surface node coordinates. You can use program SurfMeasure to do what you want. See that program's example 5 in SurfMeasures' help output.
cheers
Ziad
by
ziad
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AFNI Message Board
You can open the mask in SUMA, load it as a dataset, right click on a region and see what values are where you clicked.
by
ziad
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AFNI Message Board
francescastrappini Wrote:
-------------------------------------------------------
> Hi Ziad, thank you!
>
> You were right, the dataset was wrong. I made a
> new one and displayed into SUMA. I looked at the
> timeseries as you suggested and it seems OK. I
> have a couple of questions:
>
> 1. I can display correctly the dataset after
> 3dVol2Surf, but after p
by
ziad
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AFNI Message Board
Sorry, no windows for us. AFNI only runs under Linux and Mac OSX.
cheers
z
by
ziad
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AFNI Message Board
francescastrappini Wrote:
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> Thank you!
>
> I tried to run this command line:
>
> 3dmaskdump -mask lh.V1dorsalDMfull.1D.dset -index
> -xyz -o ALL.ts.1D v2s.lh.TS.DM.FULL.niml.dset
>
> In the output I got there are no coordinates and
> just one value (I suppose the average) for each
> vertex, so no t
by
ziad
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AFNI Message Board
Hi Tara,
>
> First, how would it be best to get this into a
> normalized space (i.e. MNI). Should I map it using
> the MNI spec files to the MNI volume, or could I
> 3dSurf2Vol it on a subject then warp the mask to
> MNI space.
Go with the first option, which would be trivial if you are using standard meshes. Load the dataset onto the MNI surfaces of matching topolog
by
ziad
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AFNI Message Board
Hi Matt,
Isaac answered the first part of your question, but as
Matthew_2 Wrote:
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> Dear AFNI gurus,
>
> I'm writing about using the AFNI matlab tool
> WriteBrik.m
>
> My intention is to run statistics in matlab and
> then write a brik that can be used in AFNI's
> viewer GUI with cluster thres
by
ziad
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AFNI Message Board
Hi Francesca,
>
> I ran this command line:
>
> ROI2dataset -prefix lh.V1dorsalDM.1D.dset -of 1D
> -input lh.V1dorsalDM.1D.roi
>
> As you suggested, I tried to add the -padd_to_node
> option to ROI2dataset and it worked!
Excellent, one down.
> Now, I would like to extract the time series from
> a functional run that I mapped to the surface,
&g
by
ziad
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AFNI Message Board
Hi Mike,
I have made changes to fix the problem but I am also puzzled because I cannot reproduce it. Could you compress the volume that causes this problem and share it with me? It would be nice to reproduce the problem and confirm that it is fixed. Either way though you should be OK with the next update. We should rebuild overnight.
cheers
z
by
ziad
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AFNI Message Board
Hi Francesca,
What was your ROI2dataset command, and why do you want to use ConvertDset on the output of ROI2dataset? You should be able to add -padd_to_node option to ROI2dataset and use that output directly without the ConvertDset step.
cheers
Ziad
by
ziad
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AFNI Message Board
Hello Michael,
That's my bad. I will fix this soon, I hope.
cheers
Ziad
by
ziad
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AFNI Message Board
Hi Xixi,
Not sure if you got that resolved, but the cause is a likely difference between the default parameters of AFNI's SurfToVol parameters. You can set those up with the Vol2Surf plugin, after you've sent AFNI the surfaces.
cheers
Ziad
by
ziad
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AFNI Message Board
Hello Francesca,
Could you email me (saadz at mail dot nih dot gov) the proc.DM script and the log of all the output from running it? That might help get to the bottom of the problem a little faster perhaps.
cheers,
Ziad
by
ziad
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AFNI Message Board
All right, we'll run tests with the data you sent us and get back to you soonish, I hope.
cheers
z
by
ziad
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AFNI Message Board
That's a little strange, it does not look like you got the update.
Can you please try again in the morning and make sure you afni -version returns a compile date of April 15th or later. If the crash persists, then the next step is to upload an archive containing data and command for me to replicate the crash.
cheers
z
by
ziad
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AFNI Message Board
Not necessarily, it should match the standard space of the input data. Is there a discrepancy between the space of input data and that of the output?
If you are not sure how to check for the space of a dataset, try : 3dinfo -space
Note that standard-space datasets are all labeled +tlrc in AFNI's native format, even if they are in MNI space for instance.
cheers
Ziad
by
ziad
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AFNI Message Board
Hello Giovanni,
No it does not sense to use AlphaSim for TBSS. Smoothing for AlphaSim is done for volumetric data (or surface-based with slow_surf_clustsim.py).
cheers
Ziad
by
ziad
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AFNI Message Board
Hi Ranjan,
You can certainly do this. I take it that you have single-subject results here so the usual approach is to map the data onto that subject's own surface model. For this work however you will need to have surface models created for that subject (with FreeSurfer for instance). If you don't want to go through that process, you can transform your subject's result to standa
by
ziad
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AFNI Message Board
Hello Gaurav,
You'll have to look into the matter yourself since ringing depends on your data and the method with which you perform the filtering. Our recommendation is in the implementation in afni_proc.py which is based on the algorithms detailed in Jo et al 2013. Ringing should not be a matter of concern since we usually bandpass and censor the data in a linear regression framework.
by
ziad
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AFNI Message Board
Hello Kai,
Hard to tell without looking in detail at what you've done. One way to get to the bottom of this is to simplify the problem to an ROI of a single voxel and very few subjects (you can acutally use 1D files as input instead of volumes). With just one voxel in the ROI, it should be easier to get things sorted out.
cheers
Ziad
by
ziad
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AFNI Message Board
Hi Uday,
I am not sure why this is happening and since @auto_tlrc is doing the trick just fine I will put this matter on the back burner particularly since we're busy teaching over the coming two weeks.
If you really want to get to the bottom of this now, consider the history of the output volume from @auto_tlrc and contrast it to the steps you've performed. You can also upload t
by
ziad
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AFNI Message Board
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