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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
Page 1 of 9
Pages: 12345
Results 1 - 30 of 270
vd.mpark Wrote:
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> Hi,
>
> This is a very naive question, I'm using afni for
> fMRI anlaysis and planning to use support vector
> machine for mvpa.
> I downloaded LIBSVM in matlab.
>
> How can I do mvpa with afni and matlab version of
> LIBSVM?
If you are familiar with Matlab, you can also consid
by
nick
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AFNI Message Board
pjkohler Wrote:
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> @Nick: Did not receive your code, see PM.
I made a second attempt.
by
nick
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AFNI Message Board
pjkohler Wrote:
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> PM sent.
Code sent.
by
nick
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AFNI Message Board
pjkohler Wrote:
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> When I try to run perform_fast_marching_mesh.m, at
> the call to perform_front_propagation_mesh, Matlab
> crashes with a Segmentation Violation error. The
> compile_mex function runs fine, but I do get a
> bunch of warnings. Have you got any experience
> with this problem? I get the same error regar
by
nick
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AFNI Message Board
pjkohler Wrote:
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> thanks for your response, and apologies for not
> responding sooner. I actually use your surfing
> toolbox a lot, so I am aware of the
> perform_fast_marching_mesh function. I was hoping
> there was an even quicker/easier, perhaps
> non-Matlab way of doing it.
Im my experience using dijkstra dist
by
nick
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AFNI Message Board
pjkohler Wrote:
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> I need to compute the pairwise distance between
> every combination of nodes on a Freesurfer
> surface. I would like to be able to get both the
> Euclidean distance and the distance along the
> mesh. I can get the Euclidean distance by loading
> the surface into Matlab and using the coordinates,
&g
by
nick
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AFNI Message Board
Greetings,
I'm the main author of CoSMoMVPA. Hopefully my responses below are helpful.
herrlich10 Wrote:
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> I'm using AFNI/FreeSurfer/SUMA tool chain, and
> CoSMoMVPA matlab package to do surface-based MVPA,
> and encountered a few problems. Any help would be
> highly appreciated.
>
> 1) According to
by
nick
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AFNI Message Board
rick reynolds Wrote:
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> Please let us know where that other 'count'
> program
> is coming from, what which OS and version you are
> running.
See related PR here:
It identifies the other 'count' binary as /usr/local/clang-3.5.0/bin/count.
It may well be the case that recent distributions of clang
by
nick
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AFNI Message Board
nick Wrote:
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> Daniel Glen Wrote:
> -------------------------------------------------------
> > The error looks like it really happens just
> before
> > with the count command,
>
> Thanks Daniel, indeed it seems a PATH issue.
> Please see
> for a Pull Request that should address the issue.
> If
by
nick
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AFNI Message Board
Daniel Glen Wrote:
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> The error looks like it really happens just before
> with the count command,
Thanks Daniel, indeed it seems a PATH issue.
Please see for a Pull Request that should address the issue.
If you think it does, could you please merge?
by
nick
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AFNI Message Board
Thanks to verbose output enabled by Yarik, the error reported is:
XIO: fatal IO error 11 (Resource temporarily unavailable) on X server ":20"
2: after 7415 requests (7398 known processed) with 0 events remaining.
See for more details.
Could this be related to afni's new detach-from-terminal-by-default behaviour that may cause a similar error (https://afni.nimh.nih
by
nick
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AFNI Message Board
rick reynolds Wrote:
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> Thanks for the details. But note that we are not
> actually maintaining
> those travis tests. I have no idea what the
> do.examples script is
> running...
All right, I re-raised the issue on github (https://github.com/afni/afni/issues/56) and ping-ed Yarik - hopefully with his help we can find
by
nick
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AFNI Message Board
Greetings,
I just noticed that ctest shows failures on the travis ci environment (see ):
23.28s$ ctest
Test project /home/travis/build/afni/afni/testing
Start 1: afni:start
1/2 Test #1: afni:start ....................... Passed 5.98 sec
Start 2: do.examples
2/2 Test #2: do.examples ......................***Failed 17.24 sec
50% tests passed, 1 tests failed out of 2
Labe
by
nick
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AFNI Message Board
Ali_Ghazizadeh Wrote:
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> I have free surfer SurfVol and a bunch of surfaces
> I want to open with SUMA and overlay my
> statistical map on it I have two issues:
>
> 1. Freesufer volume and surface is made with the
> assumption of 1mm isotropic (basically I had to
> fake the header to 1mm isotropic for freesurfer
by
nick
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AFNI Message Board
djohn Wrote:
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> Yes, our surface ROIs
> come from Freesurfer. I have been unable though to
> find any documentation though regarding the
> mris_label_calc function on FreeSurferWiki or
> elsewhere online.
If you can get the data into Matlab / Octave, the surfing toolbox can be used to erode the mask.
For example, th
by
nick
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AFNI Message Board
MCube78 Wrote:
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> I'm trying to use 3dClustSim to perform a cluster
> correction on group data. However, rather than
> being derived from the standard 1st level GLM and
> then group analysis, my group data is a set of
> 0-centered classification accuracies from an
> SVM-MVPA analysis.
>
> As things stan
by
nick
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AFNI Message Board
afniuser2014 Wrote:
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> The problem appears when stacking the two
> datasets.
>
> the node_indices are as follow...
>
> >> ds_left_right.fa.node_indices
>
> ans =
>
> 1 2 3 4 5 6 13 14
> 15 16 17 18
>
Indeed, the original code showed an er
by
nick
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AFNI Message Board
afniuser2014 Wrote:
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> I am trying to applying a cluster size based
> thresholding to my accuracy maps after MVPA
> classification (in surface space).
>
> To this end, I am using slow_surf_clustsim.py.
>
> As I did not apply any smoothing to my data, I
> think that it would be correct to use a blur
> fa
by
nick
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AFNI Message Board
afniuser2014 Wrote:
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> Thank you Nick, it worked for me.
Good, happy to hear that.
> However I had to perform some small modifications,
> I think there was a small error with the counting
> in the node_indices variable.
Could you please explain why these modifications where necessary? Without the modifications, what
by
nick
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AFNI Message Board
afniuser2014 Wrote:
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> Dear SUMA masters,
>
> I have run my first and group level analyses with
> afni/SUMA in surface space (ld = 64). Now I have a
> niml dataset for each hemisphere. [...]
> Does someone know how can I merge the right and
> left hemispheres stats niml.dset?
I've added your question to
by
nick
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AFNI Message Board
Dear Stephanie,
Stephanie Wrote:
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> I tried using 3dROIstats with the following
> command and go this error:
> 3dROIstats -nzmean -mask
> ROImask_lh_sup_post_Sync-Async.niml.dset
> 'stats.surf_individual_conditions.lh.niml.dset[8]'
> > ROIstats_IndividualValues01_lh.txt
> Error 3dROIstats: Someho
by
nick
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AFNI Message Board
cdurisko Wrote:
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> Great! Thank you. Is this documented somewhere
> and I missed it?
It seems that Bob Cox just added it to the documentation:
by
nick
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AFNI Message Board
Stephanie Wrote:
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> That you for all of your assistance.
You're welcome.
> I was able to
> make the ROI in the correct location by changing
> the spec and surface file. Now that I have a mask,
> I should be able to use 3dmaskave with this mask
> correct?
I'm not sure whether 3dmaskave supports surf
by
nick
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AFNI Message Board
Stephanie Wrote:
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> Yes now it opened.
Good.
> However, I am assuming that I
> made the ROI with the wrong file now. I identified
> the ROIs with opening suma with this command:
>
> suma -spec 118_both.spec -sv 118_SurfVol+orig
>
> However, I made the ROI with
> ROIgrow -overwrite -spec std.141.118
by
nick
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AFNI Message Board
Stephanie Wrote:
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>
> The top of the text file has this information:
> #Col. 0 Node index
> #Col. 1 ROI val.
>
> The file has two columns, one with the nodes and
> the other has what I assume should be 0s and
> 1s(however around the nodes that should make up
> the ROI it is actually 3s).
That may ind
by
nick
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AFNI Message Board
Stephanie Wrote:
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> I then used the following command for each 1D file
> to try and create a mask for the ROIs that I can
> use to extract the values (with 3 being the
> example ROI 1D file):
> ConvertDset -o_niml -add_node_index -input
> ROImask_118_lh.3.1D -prefix
> ROImask_lh_inf_post_118
>
> However,
by
nick
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AFNI Message Board
Hi Rick,
rick reynolds Wrote:
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> At any rate, I moved the NODE_INDEX list to
> be the first DA element.
>
> Thanks for pointing that out.
You're welcome, and thanks for updating the code, that's much appreciated.
best,
Nick
by
nick
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AFNI Message Board
Hi Rick,
thanks for your quick reply.
rick reynolds Wrote:
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>
>
> 1) It seems that an attribute of the read dataset
> (the
> binary aspect) is stored for the INDEX_LIST upon
> read,
> and that overrides the request to write it as
> text.
The GIFTI dataset used as input is in ASCII format; the releva
by
nick
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AFNI Message Board
Greetings,
I have two questions about how ConvertDset converts surface NIML data to the GIFTI format.
1) When using GIFTI input and using the -o_niml_asc option, the node data (in SPARSE_DATA), is in ASCII format as expected, but the node indices (in INDEX_LIST) are presented as binary. Is this intended behaviour? Is it possible to store the node indices in ASCII format as well?
2) When
by
nick
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AFNI Message Board
nick Wrote:
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> Nilufar Wrote:
> --------------------------------------------------
> -----
> > I am trying to use afni's MATLAB library to
> read
> > and write surface data in .niml.dset format.
> > Using 3dVoltoSurf, I converted volumetric data
> to
> > surface data. Now, when I use this
by
nick
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AFNI Message Board
Page 1 of 9
Pages: 12345