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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
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Thank you Taylor. I tried to run this code but got the following errors. Could you please give some advice? Thank you so much!
@chauffeur_afni \
-ulay "${anat}" \
-olay "${func_glt}" \
-set_subbricks 0 8 9
by
xiyuezh
-
AFNI Message Board
Thank you Taylor. I tried to run this code but got the following errors. Could you please give some advice? Thank you so much!
@chauffeur_afni \
-ulay "${anat}" \
-olay "${func_glt}" \
-set_subbricks 0 8 9
by
xiyuezh
-
AFNI Message Board
Hi experts,
I am trying to save images with following codes and get following error messages. Could you please help to have a look? Many thanks in advance!!
setenv AFNI_NOSPLASH YES
setenv AFNI_SPLASH_MELT NO
setenv AFNI_PBAR_GULLRANGE NO
setenv AFNI_SKIP_DYLD_WARNING YES
afni -yesplugouts $anat $func_glt \
-com 'SWITCH_UNDERLAY $anat' \
-com 'SEE_OVERLAY +'
by
xiyuezh
-
AFNI Message Board
Hi experts,
After using afni_proc.py to preprocess some resting-state fMRI data, there are always some sub-bricks become zeros in the results. I tried several times and got the same results every run. For example, one of the 3dinfo infomation of one subject:
3dinfo -verb errts.S126.tproject+tlrc.
Quote ......
-- At sub-brick #68 'S126.rs.02aptopu[68]' datum type is float: -4
by
xiyuezh
-
AFNI Message Board
Hi experts,
I am using 3dfim+ to calculate the correlations fMRI time series. I always got the warning as bellow. But I didn't find a new command to do the same thing. Could you please give some advice?
Quote
*+ WARNING: This program (3dfim+) is very old, may not be useful, and will not be maintained.
Program to calculate the cross-correlation of an ideal reference waveform
with t
by
xiyuezh
-
AFNI Message Board
Hi Gang,
Thank you for your reply.
I still think the results are the same in sub-bricks GroupAge and GroupAge t, including the clusters location and voxel numbers. Now my code is like this:
-num_glt 4 \
-gltLabel 1 Age -gltCode 1 'Age :' \
-gltLabel 2 Group -gltCode 2 'Group : 1*Singr -1*Contr' \
-gltLabel 3 GroupRisk -gltCode 3 'Group : 1*Singr -1*Contr Risk :
by
xiyuezh
-
AFNI Message Board
Thank you Gang! I got two sub-bricks 'Age' and 'Age t'. But I am wondering if I set age as a quantitive variable, how the t test runs here?
I got the exact same results after adding a space. Did I add at the right places?
-gltLabel 2 GroupRisk -gltCode 2 'Group : 1*Singr -1*Contr Risk: ' \
-gltLabel 3 GroupAge -gltCode 3 'Group : 1*Singr -1*Contr Age:
by
xiyuezh
-
AFNI Message Board
Hi experts,
I am using 3dMVM to see how age effect fMRI as a quantitative variable. I got results Age F from the code. But F scores are all positive. I am wondering if it possible to get a β coeffector from 3dMVM? Or some effector could show the data is increasing or decreasing with age.
Thank you.
My code:
3dMVM -prefix Aud_glt3 \
-bsVars "Group*Age*Risk" \
-qVars "
by
xiyuezh
-
AFNI Message Board
Hi Gang,
Sorry for ask you again and again..
I ran another 3dMVM with 4 -gltCode. The code is shown as bellow:
3dMVM \
-prefix Speech_glt3 \
-bsVars "Group*Age*Risk" \
-qVars "Age,Risk" \
-num_glt 4 \
-gltLabel 1 Group -gltCode 1 'Group : 1*Singr -1*Contr' \
-gltLabel 2 Risk -gltCode 2 'Risk : 1*Singr -1*Contr
by
xiyuezh
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AFNI Message Board
Hi Gang,
My question is that should I put the same # on the ULay and OLay options? As shown in this screenshot.
Thank you!
Xiyue
by
xiyuezh
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AFNI Message Board
Hi Gang,
Do I need to set the thresholds? The 16 sub-bricks all named as "XXX F". Or I should leave the threshold blank?
Thank you
Xiyue
by
xiyuezh
-
AFNI Message Board
Hi experts.
I have some questions about the results of 3dMVM and 3dFDR. After running 3dMVM code as bellow.
3dMVM \
-prefix SpeechMVM \
-bsVars "Group*Age" \
-qVars "Age,MoCA" \
-num_glt 1 \
-gltLabel 1 S_vs_C -gltCode 1 'Group : -1*Contr 1*Singr' \
-dataTable \
Subj Group Age MoCA InputFile \
S002 Singr 70 26 S002.rs.SpeechSeederrts.nii'[0]
by
xiyuezh
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AFNI Message Board
Hi experts,
I have some issue when trying to run 3dMVM.
It says:
Quoteupdating R_LD_LIBRARY_PATH ...
oo Warning:
Failed to load R_io.so with this error message:
Error in dyn.load(ll) :
unable to load shared object '/Users/xiyuezh/abin/R_io.so':
dlopen(/Users/xiyuezh/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/li
by
xiyuezh
-
AFNI Message Board
Hi experts,
I am using afni_proc.py to process some resting-state data. I encountered an issue when runing the script generated by afni_proc.py. The error message says:
Quote** ERROR: *** Censoring has made regression impossible :( ***
** FATAL ERROR: 3dDeconvolve dies: Insufficient data (61) for estimating 124 parameters
** Program compile date = Apr 16 2021
The 3dDeconvolve part in
by
xiyuezh
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AFNI Message Board
No, IRM2 is another user of of this computer. admin is the admin user. My user name is xiyuezh.
by
xiyuezh
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AFNI Message Board
The output:
Quotetotal 0
drwxr-xr-x 11 IRM2 admin 352 27 Apr 2017 0.29.2
Thank you!
by
xiyuezh
-
AFNI Message Board
Hi experts,
I cannot open uber_subject.py GUI on MacOS 10.14.6. Could you please help to have a look? When I try
uber_subject.py
, it says:
Quote**** failed to import PyQt4.QtGui ****
PyQt4 must be installed to run the uber_subject.py GUI
--> see the output of: uber_subject.py -help_install
Then I tried
uber_subject.py -help_install
and
brew install pyqt
The error inf
by
xiyuezh
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AFNI Message Board
Hi Rick,
Thank you for your reply. The orignal rs file size is [80 80 45 200], voxel: 3 mm x 3 mm x 3 mm, 200 volumes.
Maybe I need to set -dxyz 3 in this case?
Xiyue
by
xiyuezh
-
AFNI Message Board
Hi experts,
I am using @auto_tlrc to convert my resting-state fMRI data to MNI152. After that, about 1/3 of the files get really huge. The input data is 610MB. The shape of nii file is [100 100 80 200]. The output data is 3.71GB, with shape [161 191 151 200]. The others (2/3 participants' files) are 138.3MB, with shape [54 64 50 200]. I wonder which one is correct. Dose files usually get
by
xiyuezh
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AFNI Message Board
Yeahhh!!!! Thank you so much. Now it works. Even though I don't understand the meanning of
vox_offset 108 1 352.0
by
xiyuezh
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AFNI Message Board
Hi Rick,
Sorry I am new to AFNI. I don't understand why to remove the extension.
By using
nifti_tool -disp_hdr -infile epi.timing.nii
Before and after
nifti_tool -rm_ext ALL -overwrite -infiles epi.timing.nii
The only difference is
QuoteBefore:
vox_offset 108 1 12304.0
After:
vox_offset 108 1 352.0
Dose this affect time slicing in AFNI
by
xiyuezh
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AFNI Message Board
Hi Peter,
Sorry I made a mistake of the tparttern info. It should be seqplus.
3dTcat -prefix test18 -tpattern seqplus S018.rs.nii
3dinfo -slice_timing test18+orig
Then I got
0.000000|0.055556|0.111111|0.166667|0.222222|0.277778|0.333333|0.388889|0.444445|0.500000|0.555556|0.611111|0.666667|0.722223|0.777778|0.833334|0.888889|0.944445|1.000000|1.055556|1.111112|1.166667|1.222223|1.277778|1
by
xiyuezh
-
AFNI Message Board
Thank you Peter. Now the time slicing data is added to the file.
3dinfo -slice_timing S014.rs.nii
0.055000|0.110000|0.165000|0.220000|0.275000|0.330000|0.385000|0.440000|0.495000|0.550000|0.605000|0.660000|0.715000|0.770000|0.825000|0.880000|0.935000|0.990000|1.045000|1.100000|1.155000|1.210000|1.265000|1.320000|1.375000|1.430000|1.485000|1.540000|1.595000|1.650000|1.705000|1.760000|1.81500
by
xiyuezh
-
AFNI Message Board
Page 1 of 2
Pages: 12