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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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Hi Gang,
It has been running for almost 24 hours by now and it didn't finish yet. No dataset is output.
Phoebe.
by
pstchan
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AFNI Message Board
Hi Gang,
Thanks for your reply.
I just updated AFNI and it seems to work. However, it prompts with the following warning (after ****) after Slice 15.
Any suggestion?
Thanks in advance.
Phoebe.
*****
Loading required package: lme4
Loading required package: Matrix
Range of input data: [-0.053, 1.651]
If the program hangs here for more than, for example, half an hour,
kill th
by
pstchan
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AFNI Message Board
Hi,
I use the following 3dICC command and have an error of 'object 'runMeta' not found' below '*****'. Kindly help.
Phoebe
3dICC -prefix MDH_co2_pco2_max_decon_icc \
-mask MDH_brain_al_mask_xcereb.nii \
-model "1+Session+(1|Subj)" \
-dataTable \
Subj Session InputFile \
mdh001 CO2 mdh001_bold_co2_pco2_max_decon+tlrc'[0]' \
by
pstchan
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AFNI Message Board
Hi Gang,
Please find the following 3dinfo output of delay+orig:
Identifier Code: XYZ_61LjPrXLO5R5xxxE6TSsgA Creation Date: Sun May 17 05:16:18 2020
Template Space: ORIG
Dataset Type: Func-Bucket (-fbuc)
Byte Order: LSB_FIRST
Storage Mode: BRIK
Storage Space: 786,432 (786 thousand) bytes
Geometry String: "MATRIX(3.4375,0,0,-109.9644,0,3.4375,0,-138.4606,0,0,5.99999
by
pstchan
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AFNI Message Board
Hi,
I try to derive p-value and z-scores from the output of 3ddelay using the following command line:
3dPval -zscore -prefix out delay+orig'[2]'
However, the computation hangs and nothing comes out. Did I miss anything?
Kindly advise.
Phoebe.
by
pstchan
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AFNI Message Board
Hi,
I use FATCAT_matplot to view the correlation matrix and Fisher z matrix in the .netcc file generated by 3dNetCorr. However, I can see the FIsher Z matrix only. When I choose 'Pearson correlation' in the 'Stat' box, it prompts 'Error: invalid 'type' (character) of argument'.
Kindly help.
Phoebe.
by
pstchan
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AFNI Message Board
Hi Gang,
Thanks for your reply.
Unfortunately the '3drefit ' command couldn't append the fico parameters in the header of the dataset. But I have another question with this approach. I used the following 3dLocalBistat to output the dataset with Pearson correlation,
3dLocalBistat -nbhd 'RHDD(6)' -stat pearson -mask MASK+orig -prefix OUT A+orig B+orig
Since
by
pstchan
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AFNI Message Board
Hi Gang,
Thanks for your reply. There's only one sub-brick with pearson coef (below ****).
Any suggestions?
Phoebe.
****
Identifier Code: XYZ_juIS0my9AELnTRN2fa1AeA Creation Date: Wed Jan 10 18:38:35 2018
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST
Storage Mode: BRIK
Storage Space: 35,913,728 (36 million ) bytes
Geometry Str
by
pstchan
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AFNI Message Board
Hi,
I'm using 3dLocalBistat to generate a correlation (pearson) map between two 3D datasets. But I can't find the corresponding t or p-value. Do you know where I can dig it up?
Thanks,
Phoebe.
by
pstchan
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AFNI Message Board
Hi,
Previously I can use the following command to generate a MIP image of the MR angiographic image:
3dLocalstat -nbhd 'RECT(0,0,50)' -stat max -mask tof_al_mask_0.5+tlrc -prefix test tof_al_0.5+tlrc
Recently I update the AFNI version and I couldn't generate the MIP with the same command.
Any suggestions?
Thanks,
Phoebe
by
pstchan
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AFNI Message Board
Hi,
I use the 'Histogram' plugin to output the voxel counts of different intensity values within a roi mask. I just toggle and provide the 'Source' dataset, 'Mask' dataset and 'Output' filename in the plugin. The output numbers (values in bins and voxel counts) are slightly different from those using '3dhistog' command line below:
3dhisto
by
pstchan
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AFNI Message Board
Hi Rick,
I would like to see how different bony landmarks on the skull aligned with the radiographic baseline. I have one T1-template which has the radiographic baseline aligned horizontal. It is treated as a reference. For example, if I want to know how the supra-orbital floor is oriented with the radiographic baseline, I will align the supra-orbital floor to horizontal in another dataset
by
pstchan
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AFNI Message Board
Hi Rick,
It works now. Thanks so much.
One last thing to confirm with you. Is the convention of the Euler angles in:
(z-x-z, x-y-x, y-z-y, z-y-z, x-z-x, y-x-y)
THanks,
phoebe
by
pstchan
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AFNI Message Board
Hi Rick,
I just update the AFNI. When I type afni_util.py, the following error appears.
afni -ver
Precompiled binary linux_xorg7_64: Jul 25 2016 (Version AFNI_16.2.06)
afni_util.py
afni_util.py: not intended as a main program
Thanks,
Phoebe.
by
pstchan
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AFNI Message Board
Hi Rick,
Thanks for your reply. The following error prompts when I run afni_util.py with all 12 values from affine matrix in $mat:
afni_util.py -listfunc -join -float affine_to_params_6 $mat
Traceback (most recent call last):
File "/autofs/space/guasha_001/users/phoebe/bin/afni/current/afni_util.py", line 3586, in <module>
sys.exit(main())
File "/autofs/spa
by
pstchan
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AFNI Message Board
Hi,
I use 3dAllineate with '-warp shift_rotate' to align two datasets and the output matrix contains 12 parameters. How can I convert the parameters in the matrix to extract the Euler angles?
Thanks,
phoebe
by
pstchan
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AFNI Message Board
Hi,
I have 4 covariates included in the dataTable for the 3dLME analysis. However, 3 subjects have missing values in one of the covariates in the dataTable. How should I define the missing values and what should I put in the dataTable for those missing values?
Thanks,
phoebe
by
pstchan
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AFNI Message Board
Hi,
When I use 3dMannWhitney and 3dttest++ to work on the group comparison of the same datasets, I find that the polarity of mean difference from 3dMannWhitney is opposite to that from 3dttest++. In 3dttest++, I used default setA-setB. Would like to confirm with you if the 3dMannWhitney uses dset2-dset1 instead of dset1-dset2.
Thanks,
Phoebe.
by
pstchan
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AFNI Message Board
Hi Dan,
Bad news is that, I got another file format problem after updating AFNI to the latest version.
3dQwarp -prefix anat_fs_brain_alQ -blur 0 3 -base TT_N27+tlrc -source anat_fs_brain_al_al+tlrc
3dNwarpApply -nwarp 'anat_fs_brain_alQ_WARP+tlrc anat_fs_brain_al_al.aff12.1D' -master NWARP -source anat_fs_al+orig -prefix anat_fs_al_al
Before updating AFNI yesterday, I got
by
pstchan
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AFNI Message Board
Hi Nick and Dan,
Thanks for your expedite reply.
The anat_fs_al.nii is aligned properly with the following command only after updating AFNI to the latest version.
3dAllineate -1Dmatrix_apply anat_fs_brain_al_mat.aff12.1D -prefix anat_fs_al.nii anat_fs.nii
Both '3drefit -deoblique anat_fs_al.nii' and '3drefit -deoblique anat_fs.nii' do not work.
I recall tha
by
pstchan
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AFNI Message Board
Hi,
When I apply '3dAllineate' or 'align_epi_anat.py' to align a T1 anatomical dataset, I find a difference in the output for the same input dataset in NIFTI and BRIK format as follows:
3dAllineate -1Dmatrix_apply anat_fs_brain_al_mat.aff12.1D -prefix anat_fs_al anat_fs.nii
3dcalc -a anat_fs.nii -expr a -prefix anat_fs
3dAllineate -1Dmatrix_apply anat_fs_brain_al_m
by
pstchan
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AFNI Message Board
Hi Rick,
Thanks for your reply.
How can I get the same A1dm.x1D (with amplitudes of 1 2 3 1) as in slide 8 of AMRegression.pdf with the A1.1D (10*1:5 30*2:10 50*3:15 70*1:5)?
Kindly help.
Phoebe
by
pstchan
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AFNI Message Board
Hi,
I'm preparing a regressor .1D for the input of DM Regression. I found that the output amplitude values in the .x1D are around four-fold larger than those I put in .1D. I then used the example in the slide 8 of AMRegression.pdf to verfiy it and found that the amplitudes are as follows:
3dDeconvolve -nodata 100 1.0 -num_stimts 1 -polort -1 -stim_times_AM1 1 A1.1D dmBLOCK -x1D A1dm.
by
pstchan
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AFNI Message Board