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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 tried to overlay one hundred masks by using 3dcalc -a1 "image1" -a2 "image2" ...-a100 "image100" expr 'a1+a2*8....+a100*100' -prefix overlay
However, 3dcalc only takes -a....-z for input files but not 'a1'. How can I get around the small allowable variable number (26 from a to z) and combine one hundreds masks. Suggestions a
by
Veda
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AFNI Message Board
Hi AFNI experts,
My experiment had one between-subject continuous variable (Score) and one within-subject variable (Time) and used 3dLME to see their interaction. The model failed (see the message below). I think that the problem came from the interaction term (glt 4-6) but had no idea how to modify it. Besides, Any suggests are welcomed. Thanks!
Veda
3dLME -prefix ScorexTime -jobs 6 \
by
Veda
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AFNI Message Board
Hi Gang,
Thank you for the response.
I did try to use amean and bmean but the command gave me the same value for two levels of one factor.
Here is my script
-amean i a1 \
-amean j a2 \
-bmean i b1 \
-bmean j b2 \
The problem is that the value of a1 is the same as a2 and b1 is identical to b2. But, the four values are supposed to be totally different.
by
Veda
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AFNI Message Board
Dear AFNI experts,
I had a experiment of 2 (between-subject factor: group a and b) x 2 (within-subject factor: condition 1 and 2 ) factorial design.
I would like to know how to exact the activation value in each of the cell a1, a2, b1 and b2 in 3dANOVA3 (k=4) at the group level.
-amean and -xmean do not work.
Your suggestions will be appreciated. Thanks!
Veda
by
Veda
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AFNI Message Board
Hi Gang,
With all respect to your previous suggestion, my main concern is about Why AFNI treated frontal and parietal lobe as one big cluster without respecting the anatomical boundary. I thought that the problem might be more about smoothing rather than about the effect size. Would you agree?
by
Veda
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AFNI Message Board
Hi Gang,
Thanks for the response.
I checked the results at the single subject level and found the same thing (a large significant chunk). The table below was extracted from the results from simple t-test (condition A vs. baseline) for one subject at p value of 0.05.
# AFNI interactive cluster table
# 3dclust -1Dformat -nosum -1dindex 10 -1tindex 11 -2thresh -1.967 1.967 -inmask -dxyz=1 1.
by
Veda
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AFNI Message Board
Hello AFNI experts,
When I viewed cluster results after conducting 3dRegAna, there was a large significant cluster with 9190 voxels. The significant cluster covered both frontal lobe and parietal lobe. The image file for each subject was smoothed at 8mm. How can I get AFNI to report the results in reasonably restricted area rather than in a big chunk? Thanks!
Best,
Veda
by
Veda
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AFNI Message Board
Hello Daniel,
Thank you for this helpful post. However, the output of 3dExtrema can only be saved as image file.
Is it possible to save the peaking coordinates from 3dExtrema as text files? Your suggestions will be appreciated.
Veda
by
Veda
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AFNI Message Board
Hi Gang,
Thanks for the suggestion on the polort.
I am sorry that I did not say things right about my first question.
The negative connectivity was observed between the seed and the rest of the brain not the seed region itself.
Veda
by
Veda
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AFNI Message Board
Dear AFNI experts,
I have followed the website below to do seed functional connectivity.
I tried two different regression models: One is to include the regressor of experimental condition, the detrended time series of seed region and their interaction regressor (seed X conditions); and the other is to include everything except the detrended time series of seed region. One main difference
by
Veda
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AFNI Message Board
Hello Rick,
I am sorry to come back to this post so late. Somehow, I was not notified by any email alert about your reply.
360 TRs are from four separate runs. The stimulus lasted about 60 seconds in each run. In this case, what is polort for 3dDetrend and for 3dDeconvolve? The new script for PPI looked so different from mine which was created by the suggestions in this website (https://afni.
by
Veda
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AFNI Message Board
Dear AFNI experts,
I followed the procedure of gPPI (see the link below) to do connectivity analysis for an block-design fMRI experiment.
Below is my script:
3dDetrend -polort 1 -prefix ${connf}/${roi}/${1}.${roi}.Seed_dtr.1D ${connf}/${roi}/${1}.${roi}.sSeed.1D\'
1dtranspose ${connf}/${roi}/${1}.${roi}.Seed_dtr.1D ${connf}/${roi}/${1}.${roi}.Seed_dtr_t.1D
waver -dt 2 -GAM -inline
by
Veda
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AFNI Message Board
Hi Rick,
I am sorry for the confusion. I really appreciate your patience on this.
My EPI images (*.hdr) can be read by 3dTcat but my anatomical images (*.IMA) cannot be read by 3dTcat.
Veda
by
Veda
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AFNI Message Board
Hi Rick,
But, my T1 images are with filename extension of "IMA" not "hdr". So, the error said "FATAL ERROR: Can't open dataset raw_data/subj01/T1P/Y-S_CHEN.MR.NCU_WU.10.100.2010.12.20.12.10.48.125000.86003572.IMA"
For 3dTcat to work on T1, could you please suggest something?
Thanks!
Veda
by
Veda
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AFNI Message Board
Hi Rick,
3dTcat -prefix epi.tcat raw_data/$subj/F{$block}P/*.hdr
The above line works but cannot read T1 image (*.IMA). An error occured:
Can't open dataset raw_data/subj01/T1P/Y-S_CHEN.MR.NCU_WU.10.100.2010.12.20.12.10.48.125000.86003572.IMA
Dimon -gert_create_dataset -quit -file_type AFNI \
-infile_pattern "raw_data/$subj/F{$block}P/*.hdr"
The above two lines cannot
by
Veda
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AFNI Message Board
Hello Rick,
My files are "ni1". If so, why they are deemed as invalid by Dimon?
Veda
by
Veda
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AFNI Message Board
Hello Rick,
Thanks for the reply.
However, it turned out that I need to use following line to convert my data into brick:
Dimon -GERT_Reco -gert_nz 33 -gert_to3d_prefix $subj.r0$block -infile_prefix raw_data/$subj/F{$block}P/* -quit -gert_filename raw_data/$subj/F{$block}P/tmp$block -overwrite
However, the error message says:
invalid option <raw_data/subj01/F1P/afR223622001-0002-00001-
by
Veda
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AFNI Message Board
Dear AFNI users,
I m totoally new to AFNI.
I try to apply to3d on my data for further analysis. It seems that input data is with *.DCM extension. However, my fMRI data from Simons only come in *.IMG and *HDR. Therefore, the error messages shows that How can I fix this issue? Could anyone suggest a image converter for me? Or, is there some other way to fix the problem? Thanks!
Veda
by
Veda
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AFNI Message Board