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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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Pages: 12
Results 1 - 30 of 33
Sorry, i mean which transformation (affine, other?)
thanks
P.
by
chpiero
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AFNI Message Board
Dear afni experts,
what kind of spatial normalization is used to perform spatial normalization in mni?
thanks,
Piero
by
chpiero
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AFNI Message Board
Hi afni experts,
using the align_epi_anat command as shown below, my question is the found transformations (Slice timing, motion correction, reg EPI to ANAT, reg EPI to MNI) are applied one at a time or all together?
Tanhks
align_epi_anat.py \
-anat ANAT.nii.gz \
-epi EPI_r01.nii.gz \
-child_epi EPI_r??.nii.gz \
-epi_base 0 \
-tshift_opts -tpattern @slice_t
by
chpiero
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AFNI Message Board
Is it possible to make GLTs outside 3dDeconvolve?
I ask this because I would not always like to use the GLM if I just want to recalculate the tests with combinations of different conditions.
Thanks
by
chpiero
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AFNI Message Board
Hello afni experts,
how can I with afni, having the time of a complex stimulus formed by: text, scene of a film, cross of fixation, eliminate the contribution of the stimulus "text" only?
For each stimulus I have onset and duration time.
In practice I should have a residual timecourse where the contribution of the text has been removed inside. Do you have an example?
Maybe you
by
chpiero
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AFNI Message Board
Hello everyone,
it is possible with AFNI to make a spatial correlation between two maps of ICA components. in practice I applied melodic ICA on 162 subjects but now I should extract only the DMN components of each and do a separate statistical analysis. Anyone know how I can do that?
thanks
by
chpiero
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AFNI Message Board
Ok asap.
Is possible have some help documentation about right menu (for example what does it mean "cluster linkage"?)
There is a little graphic problem i've 169 ROI with each label but when display the matrix i don't see all labels, i suppose because there are so many. It's possible change size of label?
thanks
Piero
by
chpiero
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AFNI Message Board
Hi,
below the list of file:
FCN004_3dNetCorr_CorrMat_000.netcc
FCN004_3dNetCorr_CorrMat_000.niml.dset
FCN004_3dNetCorr_CorrMat_000.roidat
the files are created by 3dNetCorr command.
thanks,
Piero
by
chpiero
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AFNI Message Board
Hi Afni experts,
i try this command @FATCAT_matplot_shiny but i've an error:
Loading required package: tools
Error in basename(file.list2) : a character vector argument expected
Calls: <Anonymous> ... sourceUTF8 -> eval -> eval -> ..stacktraceon.. -> basename
Execution halted
the netcc file inside the directory contain this:
# 4 # Number of network ROI
by
chpiero
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AFNI Message Board
Dear Afni experts,
We have a question regarding the interpretation of values after running a MVM.
The model used the beta values from GLM maps. the MVM analysis is based on a 2x2x3 model where there are 2 groups (OMT - SHAM), 2 tasks (Heart - Sound) and 3 time points (t0 - t1 - t2) and additional covariates, i.e. sex and age. So the MVM model is the following:
bs: Groups*age*Sex
ws: task*ti
by
chpiero
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AFNI Message Board
first step "suma -i Net_000.gii & "
second step "DriveSuma -com surf_cont -view_surf_cont y -com surf_cont -surf_label Net_000.gii -switch_cmap amber_monochrome -Dim 1.0 "
in attach you find the output (step1 & step 2). No terminal error message
by
chpiero
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AFNI Message Board
"That visualization demo requires running the Do_00... script. Have you done that? "
Yes but don't work.
by
chpiero
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AFNI Message Board
Hi afni experts,
I've the error below when lunch "tcsh Do_06_VISdti_SUMA_visual_ex1.tcsh" in step 2.
Someone have the solution?
Bests,
Piero
(You can change max. wait time with env. SUMA_DriveSumaMaxWait)
PO: plugout 'plugout_drive' has broken connection!
: iochan_goodcheck: no longer alive
Error SUMA_IO_args_2_spec:
Could not locate surface Net_00
by
chpiero
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AFNI Message Board
Hi afni experts,
Is possible to read in afni a dicom file which contains two echos (for examples first echo BOLD signal and second ASL signal) and then separate them into two different dataset (2 files)?
Bests,
Piero
by
chpiero
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AFNI Message Board
Dear AFNI experts,
After having obtained the output from 3dMVM how i can choose the best F statistical model to be used for post-hoc comparisons?
you can find below both the MVM command script and the "3dinfo" command output. As you can see there are different F statistical models and we want to define which model is the most appropriate. Is there a way to compare all the different
by
chpiero
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AFNI Message Board
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 15.5.0
version: Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64
distribution: 10.11.5 x86_64
number of CPUs: 8
apparent login sh
by
chpiero
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AFNI Message Board
Hi afni experts,
i use 3dMEMA and i have this error:
----------------------------------------------------------------------
oo Warning:
Failed to load R_io.so with this error message:
Error in dyn.load(ll) :
unable to load shared object '/usr/local/afni/R_io.so':
dlopen(/usr/local/afni/R_io.so, 6): Symbol not found: ___intel_sse2_strcat
Referenced from: /usr/local
by
chpiero
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AFNI Message Board
Hi everybody,
I'm trying to estimate the delay between ROIs timecourses, something similar to the Hilbert delay but performed on .1D files containing fmri signals extracted from ROIs. Can you help me?
thanks,
Piero
by
chpiero
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AFNI Message Board
Thanks, Daniel. I already considered 3Ddelay but what I'm trying to do here is to use a voxel wise reference time series: I have a 3D+time dataset A and a 3D+time dataset B and want to compute the delay between the timeseries of voxel(i,j,k) in A and the time series of the corresponding voxel in B, reiterating this for all voxels….
by
chpiero
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AFNI Message Board
Dear afni expert,
I'm trying to estimate the temporal delay between corresponding voxel time series of two input 3D+time datasets. In other words something similar to 3dTcorrelate but, instead of the correlation coefficient, I'd like to generate a delay map. Do you know if there is an easy way to do it in AFNI ?
Thank you in advance for any help
Piero
by
chpiero
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AFNI Message Board
Dear Afni expert,
i've used 3dcopy to convert a nifti file to HEAD/BRIK, but after the upgrade to Version AFNI_2011_12_21_1014 (Precompiled binary macosx_10.7_Intel_64: Mar 27 2014), i've noticed that obliquity parameters (3dinfo) is set to 0 while in the original nifti file it has a different value. Probabily this is due to the upgrade version because before that it worked with the s
by
chpiero
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AFNI Message Board
Dear Afni experts,
i have calculated a coherence matrix between 36 ROIs (dimension of matrix is 36x36) outside of Afni and i want to convert this matrix file.txt in a dataset HEAD/BRIK (like the output dataset of @ROI_Corr_Mat) , is it possible ?
Thanks,
Piero
by
chpiero
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AFNI Message Board
Hi afni experts,
Is possible to calculate coherence between two timeseries?
Thanks,
Piero
by
chpiero
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AFNI Message Board
Hi afni experts,
I want make deoblique option with 3dWarp but my EPI isn't isovoxel when i run
this command my output file is a isovoxel EPI. Is possible have non isovoxel EPI as output?
Chpiero
by
chpiero
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AFNI Message Board
Hi afni expert,
i want open two files (one underlay and one overlay) with afni command by terminal, is possible?
chpiero
by
chpiero
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AFNI Message Board
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Pages: 12