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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 am confused about the mask coordinates. In Talairach space, locations in the left hemisphere have negative x coordinates, while locations in the right hemisphere have positive x coordinates. However, left/right coordinates seem to have been flipped in afni. For example, the Talairach coordinates of right Fusiform Face area were [-34.5, +43.5, -18.5].
Thanks a lot in advan
by
jiaxin
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AFNI Message Board
Hi Gang,
In the 3dDeconvolve help files,
==> ** Despite the name, you can use 'BLOCK' for event-
related analyses just by setting the duration to
a small value; e.g., 'BLOCK5(1,1)'.
Therefore, I am not sure which ‘BLOCK’ (BLOCK(1,1) or BLOCK5(1,1)) is more suitable in my experiment.
Thank you very much
by
jiaxin
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AFNI Message Board
Hi afni experts,
I have one question regarding 3dDeconvolve. My experiment is slow event-related design, and duration of each event does not exceed one second. In the 3dDeconvolve help file, there are 2 variants of BLOCK: BLOCK4 and BLOCK5, and the latter is delayed by about 1 second from the former. However, I am not sure which ‘BLOCK’ (BLOCK4 or BLOCK5) is more suitable in my experiment.
by
jiaxin
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AFNI Message Board
Hi Daniel,
I also have one question regarding alignment across two sessions.
Firstly, I aligned all epi datasets to each session's own anatomical (E1->A1, E2->A2). Secondly, I used align_epi_anat.py to align the A2 from the second session to the A1 from the first session (A2->A1), and then computed their transformation matrix. Lastly, I used 3dAllineate and the transformatio
by
jiaxin
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AFNI Message Board
Hi Daniel,
Because these masks were draw in the volume, it is not sure whether the white matter is included in these masks.
Furthermore, how to remove the white matter from each mask?
Thanks a lot in advance.
-Xin
by
jiaxin
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AFNI Message Board
Hi Daniel,
Thank you so much for your assistance!
I ran makeline3D.csh, then it did work. However, there is only 1 voxel in ROI.
Furthermore, how to draw a sphere ROI according to coordinates and radius (i.e., 40 voxels) ?
Thank you very much again!
-Xin
by
jiaxin
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AFNI Message Board
Hi AFNI experts,
I have one question about how to draw ROIs in the volume.
How to draw a line to connect the two ROIs according to the peak coordinates? And then how to find each ROIs along the line?
Thanks a lot in advance.
-Xin
by
jiaxin
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AFNI Message Board
Hi Gang,
I have a question regarding how to use 3dttest or 3dttest++.
Each participant had a dataset with classification accuracy after I finished searchlight, but now I need to select voxels that their classification accuracy significantly higher than the chanve level (0.5) from every participant. I want to do the analysis of each participant, not a group analysis.
My script and Warni
by
jiaxin
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AFNI Message Board
Hello,
I am trying to create ROIs in surface space according to the coordinates, similar with the 3dUndump in AFNI. But I am not sure how to do this in SUMA.
Thanks!
Xin
by
jiaxin
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AFNI Message Board
Hello Daniel,
Thank you very much for your quick response.
I ran below (with the command lines) before 3dmaskave, then it did work (no warning).
float_scan -fix cl_sigpc+tlrc.BRIK > cl_psc+tlrc.BRIK
rm -f cl_sigpc+tlrc.BRIK
mv cl_psc+tlrc.BRIK cl_sigpc+tlrc.BRIK
And I have another question about how to use 3dsynthesize.
The warning message I keep getting is(all sub-briks):
*+W
by
jiaxin
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AFNI Message Board
Hi everyone,
I have a question regarding an warning related to 3dmaskave.
My script and Warning Message with 3dmaskave:
3dmaskave -mask rFFA+tlrc -quiet lqj_sigpc+tlrc
++ 3dmaskave: AFNI version=AFNI_2011_12_21_1014(Jun 26 2015) [64-bit]
+++38 voxels survive the mask
*+ Warning: file ./lqj_sigpc+tlrc.BRIK: fixed 1166880 float errors.
Thank you so much for your assistance!
Xin
by
jiaxin
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AFNI Message Board
Hi AFNI experts,
I'm totally new in afni. I have one question about how to use 3dsynthesize. Thanks a lot!
The warning message I keep getting is:
*+WARNING: clexp_int+tlrc[0] scale to shorts mean misfit error =12.4% -- *caution
... ...
*+WARNING: clexp_int+tlrc[1] scale to shorts mean misfit error =10.6% -- *caution
... ...
My script is:
3dsynthesize -matrix X.xmat.1D -cbuc
by
jiaxin
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AFNI Message Board
Hi rick,
I don't find any slice timing information in HEAD file, so I should use '-tpattern'.
However, I have two kinds of slice orders in experiment. In the first four runs, the slice order is 2, 4, 6, 8, ......,30, 32,1, 3, 5, 7,......,29,31; and in the back four runs, the slice order is 31,29,27,25,....3,1,32,30,28,26,......4,2.
The script is
#!/bin/tcsh
afni_pr
by
jiaxin
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AFNI Message Board
Hello rick,
I have a question about 3dTshift.
The code is 3dTshift -tzeros 0 -quintic -prefix pb01.cxexp.r01.tshift pb00cxexp.r01.tcat+orig, but a warning: dataset is already aligned in time! output dataset is just a copy of input dataset.
My experiment is slow event-related design, so slicing timing correction is very important. Dataset: 3T Siemens, slices number: 32, scanning sequence: in
by
jiaxin
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AFNI Message Board
Hi rick,
I have one more question, why are the ''num TRs per stim" not the same? The last trial is 6 for each category, and the others are 14 or 13.
The preprocessing script:
#!/bin/tcsh
set sid = cl # subject to process
set subj = $sid.results # subject ID for result (align case)
afni_proc.py -subj_id $sid
by
jiaxin
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AFNI Message Board
Hi rick,
% afni -ver
Precompiled binary linux_openmp_64: Jun 26 2018 (Version AFNI_18.1.33)
% ls -l @ss_review_basic
-rw------- 1 vision_lab vision_lab 12095 July 26 18:20 @ss_review_basic
% head -n 1 @ss_review_basic
#!/bin/tcsh
% which tcsh
/usr/bin/tcsh
% ls -l /bin/tcsh
lrwxrwxrwx 1 root root 13 Jun 22 2012 /bin/tcsh -> /usr/bin/tcsh
Thanks,
- jiaxin
by
jiaxin
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AFNI Message Board
Hi rick,
I'm totally new in afni. I have a similar error about the "permission denied".
When running the preprocessing script, everything runs smoothly until:
./@ss_review_basic
./@ss_review_basic: Permission denied
Then running tcsh @ss_review_basic
gives:
subject ID : cl
TRs removed (per run) : 0
num stim classes provided : 12
final anatomy d
by
jiaxin
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AFNI Message Board
Dear AFNI experts,
I'm totally new in afni. Here are some questions about how to write truly stimulus timing file and I really hope you can help me. Thanks a lot!
My experiments is slow event-related design. There are 8 runs and 11 types of stimulus conditions in a scanning session, each run consisted of 24 trials (1 trial=14s). However, the number of stimulus condition is different in
by
jiaxin
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AFNI Message Board