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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 AFNI Experts:
I ran 3dMVM to analyze my data, which includes three groups. Afterwards, I ran 3dFWHMx and 3dClustSim. Can I use the same cluster threshold for the post-hoc t-tests?
Thanks,
Lisa
by
antoinel
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AFNI Message Board
Hi AFNI Experts,
I am getting the same error message:
++ Loading -insdat datasets
** FATAL ERROR: dataset grid too big -- must recompile to use shorts as indexes :(
** Program compile date = Jul 25 2018
** FATAL ERROR: ===== 3dClustSim command failed (( =====
** Program compile date = Jul 25 2018
What is the resolution without resampling my data?
Thanks,
Lisa
by
antoinel
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AFNI Message Board
Is the mask created from SaveMsk in the AFNI GUI a binary mask? If not, how do I change the mask to a binary mask?
by
antoinel
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AFNI Message Board
Hello AFNI Experts,
How do I add my 3dClustSim results to my overlay dataset's header? Below is my 3dClustSim code.
#!/bin/tcsh
module load AFNI/18.2.05-intel-2016a-Python-2.7.11
3dClustSim -mask mask2IIT2.nii \
-nodec -acf 0.33910251948052 3.23117512987013 7.8156487012987 -iter 10001 \
-pthr .05 .025 .01 .005 .001 \
-athr .05 .025 .01 .005 .001 \
-prefix clusterFA_table
by
antoinel
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AFNI Message Board
Thanks Daniel and Gang. It is working now. I was using the wrong niftii file.
by
antoinel
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AFNI Message Board
I am using 3dMVM to analyze three groups. See the script below. How do I limit the voxels to white matter only in the output? See the output image below.
3dMVM -prefix Test5.nii -jobs 24 \
-bsVars SDS_deficit \
-qVars "Age,Sex,RMS_rel_av" \
-num_glt 3 \
-gltLabel 1 'nds-ds' -gltCode 1 'SDS_deficit: +1*0 -1*1' \
-gltLabel 2 '
by
antoinel
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AFNI Message Board
How do I interpret the 3dMVM output image from my message on November 6?
by
antoinel
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AFNI Message Board
Hello,
I used 3dSeg to segment the brain volume into tissue classes from my 3dMVM output in the previous message. See the code below.
3dSeg -anat Test3.nii -mask AUTO \
-classes 'CSF ; GM ; WM' \
-bias_fwhm 25 -mixfrac UNI -main_N 5 \
-blur_meth BFT \
-prefix Test3WM
I received the following errors and warnings. How do I fix these err
by
antoinel
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AFNI Message Board
Thanks again, Gang. I used the following 3dMVM code to analyze the three groups.
3dMVM -prefix Test3 -jobs 24 \
-bsVars SDS_deficit \
-qVars "Age,Sex,RMS_rel_av" \
-num_glt 3 \
-gltLabel 1 'nds-ds' -gltCode 1 'SDS_deficit: +1*0 -1*1' \
-gltLabel 2 'nds-hc' -gltCode 2 'SDS_deficit: +1*0 -1*2' \
-gltLabel
by
antoinel
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AFNI Message Board
I am analyzing 3 groups with 2 covariates. Can I use 3dMEMA or 3dLME for this analysis? If yes, which is more suitable for this analysis, 3dMEMA or 3dLME?
by
antoinel
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AFNI Message Board