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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 2 of 3
Pages: 123
Results 31 - 60 of 81
Hello Bob and Gang,
Fantastic, I wondered whether it was possible but also thought of this alternative option and you wrote the code!! Thanks very much.
Cheers
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Dear all,
Is it possible to perform duration modulation with the SPMG1 basis function instead of dmBLOCK?
In other words,
3dDeconvolve -num_stimts 1 -polort -1 -nodata 200 0.5 -stim_times_AM2 1 A1.1D SPMG1 -x1D stdout: | 1dplot -stdin -THICK -del 0.5
where A1.1D = 10:5 30:10 50:15 70:5
Best,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello
You need to run only one big 3dDeconvolve modelling all the trials individually, i.e. the 32*2*6 in one single model. However, you could also run 3dDeconvolve and 3dLSS for each individual run since 3dDeconvolve is only used to create the design matrix for 3dLSS. Of course, 3dLSS will have to be run for each run separately too.
Hope this helps,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello,
You don't have to run 3dDeconvolve 64 times. The stim_times_IM option in 3dDeconvolve will generate one regressor per trial (i.e. single trial). Check the design matrix with 1dplot or look at the X.jpg image (note you have written X..jpg with two dots). Then, 3dLSS will estimate the betas for each single trial via Ridge Regression as recommended in Mumford's paper instead of t
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello,
Have you downloaded the data of the demo through @Install_3dPFM_Demo?
Also please note that some R-functions are required for running 3dPFM. More details in
Hope this helps,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello,
The answer depends on the type of data/variable you want to input to MVPA and LibSVM. If you want to input the effect size (i.e. the betas) for each stimuli, you can compute them with 3dDeconvolve using --stim_times_IM. It might be a good idea to run 3dREMLfit to account for serial correlations. However, if the trials were highly correlated (e.g. in a fast event-related design), the pr
by
Cesar Caballero Gaudes
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AFNI Message Board
Dear Daniel and Nick,
I agree with Daniel in that it would not be very difficult to create this function since it is basically shuffling the phase of the FFT of the voxel time series, and then apply the inverse FFT. Meanwhile, I've created my own 3dFFTshuffle using the R interface to create AFNI compatible programs, as described in 3dRprogDemo. Please contact me (c.caballero@bcbl.eu) so t
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Daniel,
I don't know why but I didn't receive your reply. I've just realised that 1dgrayplot is the function I need.
Thanks for your comment,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello AFNI gurus,
I would like to do the convolution of a 3d+time dataset that contains stimulus times series for each voxel (e.g. this could be the output of a whole-brain 3dTfitter or 3dPFM analysis) and an IRF that is saved as .1D file. I tried to use 3dConvolve but without too much luck. Here is the command (although I tried several combinations of options considering that convolution is c
by
Cesar Caballero Gaudes
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AFNI Message Board
Dear AFNI community
I am forwarding this message from the direction of the Basque Center of Cognition, Brain and Language.
Cesar
-------------
RESEARCH FACULTY POSITIONS at the BCBL- Basque Center on Cognition Brain and Language (San Sebastián, Basque Country, Spain) www.bcbl.eu (Center of excellence Severo Ochoa)
The Basque Center on Cognition Brain and Language (San Sebastián, Ba
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello,
I would like to create a grayscale image with all the voxel time series of a dataset, which I have now created as a large .1D file using 3dmaskdump (> 20000 voxels, 300 time points). At the moment, I am using aiv, but I cannot resize (or strecht) the image so that the horizontal size representing the time axis becomes larger. Is it possible to achieve that with aiv or should I use an
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello Emily,
1) It is recommendable that all regressions are carried out in one step, i.e. including the CSF and WM and bandpass regressors together. In such a way, the fitting can properly deal with possible correlations between the regressors. This is properly handled by several AFNI programs, for instance, 3dTproject. Otherwise, you will have to orthogonalize the regressors of the second s
by
Cesar Caballero Gaudes
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AFNI Message Board
Dear all,
I have got two EPI datasets from different sessions and I would like to align the dataset of session 2 to the dataset of session 1 with as less interpolation as possible. The datasets have been already corrected for motion (i.e. no need of 3dVolreg). Which program would you recommend: 3dAllineate or align_epi_anat.py? Thanks in advance.
Best,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi all,
I have an issue of compatibility between AFNI and FSL. I've done a Group ICA analysis with MELODIC in FSL, and I wanted to create a bucket with a subset of the maps of the components of interest. Selecting the volumes is easier and quicker in AFNI with 3dbucket, so I did as follows:
3dbucket -prefix melodic_IC_good.nii.gz 'melodic_IC.nii.gz[0,1,3,4,7,8,11,12,13,14,18]
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi there,
I tried with the option -read and I still got all zeros. I didn't try with the option -ztest. I'm sorry I didn't post it back.
I'm away this week and I cannot access this data remotely, but I will follow any post and let you know next week.
Best,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Bob,
I copy all datasets to a local directory, but this did not solve the problem. I can still see the A_GRP_ICORR+tlrc volume but it is all zero.
Any other suggestion?
This is the output of 3dGroupInCorr
$ 3dGroupInCorr -setA FOGp.grpincorr.niml -setB FOGm.grpincorr.niml -verb -sendall
++ 3dGroupInCorr: AFNI version=AFNI_16.0.01 (Jan 27 2016) [64-bit]
++ Authored by: Cox, the M
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Bob,
IT staff told me that the data files are on a remotely mounted filesystem. This is the way they are mounted:
192.168.152.20:/root_vdm_1/home on /bcbl/home type nfs4 (rw,addr=192.168.152.20,clientaddr=192.168.152.254)
192.168.152.20:/root_vdm_1/data on /bcbl/data type nfs4 (rw,addr=192.168.152.20,clientaddr=192.168.152.254)
The network connection to the NSF is a 20Gb ethernet tru
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Bob,
It must be option (2) rather than (3) ;) and (1). The individual subject results are also 0. Any ideas why?
The datasets were preprocessed with a self-tuned version of afni_proc.py including WM local regression and spatial blurring with 3dmerge (FWHM 6mm) and nonlinear warping to TT_N27. In other words, nothing really special I believe. I can generate reasonable FC maps with InstaCo
by
Cesar Caballero Gaudes
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AFNI Message Board
Dear all,
I would like to run 3dGroupInCorr for a comparison between 2 groups (2-sample t-test with no covariates). For that, I did as shown in slide 23 of
# Create GroupInCorr structures for each Group
ggg=
for subject in $subjects_FOGp
do
ggg=$(echo $ggg pb05.${subject}.anaticor.blur+tlrc.HEAD )
done
3dSetupGroupInCorr -mask full_mask.frac0.85_TT_caez_ml_18+tlrc. -prefix FOGp -
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Gang,
Can quantitative covariates (e.g. age) be also input with 3dANOVA?
Thanks,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Dear all,
I would like to perform several statistical tests between 3 different groups of subjects. As input data, I am considering two options:
a) 3D volumes (e.g. seed-voxel correlation maps), and b) functional connectivity matrices generated with @ROI_corr_mat, which thus are available in BRIK and 1D. In some tests, I would also like to consider additional quantitative covariates (e.g. ag
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi all,
I'd would like to use plugout_drive to save images of all slices in separate jpeg files. I could create a FOR loop for the coordinates, move "SET_IJK" and save the images one by one.
However, I was wondering whether there is a simpler way using SAVE_ALLJPEG, but how can I tell the program to open the image sequence viewer to 'Rec' Stay ON and move from slice X
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Daniel,
No problem at all. By inline inverse warp, do you mean 3dNwarpApply with -nwarp as shown in the help ??
-iwarp = After the warp specified in '-nwarp' is computed,
invert it. If the input warp would take a dataset
from space A to B, then the inverted warp will do
the reverse.
++ The combination &
by
Cesar Caballero Gaudes
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AFNI Message Board
Dear all,
I found a very strange behaviour when applying an inverse transformation to a volume with ROI masks that was created in the MNI space and perfectly fits the areas of interest in the MNI152_T1_2009c+tlrc template
When I project the ROI volume back to the subject space with the following command
3dNwarpApply -short -master 'PrestofRegDTRCRRVTcor+orig.[0]' -nwarp Presto
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi,
I have a tiny problem with SUMA. The text of the SUMA window (e.g. with the name of the area) does not refresh as I move the cursor. Consequently, the text keeps overlapping and it is difficult to read it.
Is there any problem with my installation? I am running in MacOsX 10.9.5.
cesars-MacBook-Pro:suma_TT_N27 cesar$ afni -ver
Precompiled binary macosx_10.7_Intel_64: Apr 9 2015 (Ve
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Daniel,
Thanks very much. The script was very helpful - I should have remember it from the AFNI bootcamp.
Best,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi all,
I would like to plot the results of Functional Connectivity graph analysis with SUMA.
Briefly, this is what I did so far
1) the TT_N27 template was used for normalization and ROIs were selected from TT_caez_ml_18 parcellation.
2) I computed the connectivity matrices with @ROI_Corr_Mat considering only the first 90 regions of the parcellation, i.e. excluding the cerebellum.
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Rick,
I found the following article that seems to indicate what you suggest:
I assume 3dDeconvolve implements an adaptive two-stage FDR approach as it is described in 3dFDR. According to the paper, would this mean that a two-stage FDR approach might not be appropriate if statistical values are very high in the entire brain?
Dataset was acquired at 7T and preprocessed as follows
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello AFNI,
I would like to ask for your expertise regarding FDR !!
After 3dDeconvolve I see that the FDR-corrected q-values are smaller than the uncorrected p-values. Does this make sense? It is a single-subject analysis with a simple model including one ROI time series and the motion parameters. I use a mask for within-brain voxels.
Maybe it is fine, but I would like to hear your opini
by
Cesar Caballero Gaudes
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AFNI Message Board
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Pages: 123