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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, pt-
Thanks for your reply, I have solved it.
I guess that I run two parallel analyses.
Suma worked out and it can talk to AFNI.
Thanks a lot!
Dan
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Dan
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AFNI Message Board
Dear AFNI experts,
I want to visualize my results using suma, but I found a difference between the suma results and the actual results(as attached).
Curiously, suma showed some brain regions that the actual results did not, like some yellow areas in the red circle.
I don't know why this happens, could you give me some suggestions?
Thanks!
Dan
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Dan
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AFNI Message Board
Dear AFNI experts,
I am attempting to download an anatomical mask on MNI space, Could you give me some suggestions?
I tried this command:
whereami -prefix lba41mask -mask_atlas_region 'TT_Daemon::Left Brodmann 41'
3dresample -dxyz 3.0 3.0 3.0 -prefix LBA41 -inset lba41mask+tlrc
But when I tried to extract the time series, the time file was empty.
The warning was t
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Dan
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AFNI Message Board
Thank you very much.
I have reprocessed my datasets on the MNI space.
Thanks again for your help!
Dan
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Dan
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AFNI Message Board
Hi Daniel,
I'm sorry to reply so late...
I use "-preserve" to move the data with 3dfractionize:
3dfractionize -template ../ffa_ppa/0815/MNI152_T1_2009c+orig -input FIRST_HOUSEFC_FACEFC_rppa+tlrc -warp TT_N27+tlrc -preserve -clip 0.2 -prefix MNI_FIRST_HOUSEFC_FACEFC_rppa.
The warning was: this option requires short- or byte-valued input dataset!New dataset output failed. (at
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Dan
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AFNI Message Board
Hi, AFNI expert,
I had a problem with “3dfractionize”.
I tried the approaches:
3dfractionize -input FIRST_HOUSEFC_FACEFC_rppa+tlrc -warp TT_N27+tlrc -prefix MNI2009c_FIRST_HOUSEFC_FACEFC_rppa \
-template ../ffa_ppa/0815/MNI152_T1_2009c+orig
The form of was rather than , I can’t find the activated brain regions. It was just a pure red area.
Attached is the picture I have of MNI20
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Dan
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AFNI Message Board
Thank you so much for your help.
I tried the command :
3dfractionize -input FIRST_HOUSEFC_FACEFC_rppa+tlrc -warp TT_N27+tlrc -prefix MNI_FIRST_HOUSEFC_FACEFC_rppa -template MNI152_2009_template+tlrc
But it was warning: Template is not in +orig view (as attached)
I don't know why this happens...Could you give me some suggestions?
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Dan
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AFNI Message Board
Dear AFNI experts,
I am attempting to open a functional map of task-related activity on the MNI template. Preprocessing and group analyses were performed based on TT_N27 space.
How to accurately convert TT_N27 space to MNI space?
Thank you for your help,
Dan
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Dan
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AFNI Message Board
Hi AFNI experts,
Is there any way in AFNI/SUMA to visualize the overlapping of two brain mappings? One-color brain mapping represents one condition, similar to the figure in the attachment.
Thanks in advance,
Dan
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Dan
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AFNI Message Board
Hello,
Recently I encountered a problem about Talairach coordinates in different AFNI versions. The brain region of the same coordinates is different using “where am I” in different versions.
For example:
The Version AFNI_18.3.15 ‘Augustus’ in linux_ubuntu_16_64:
Talairach coordinates: (-38,-14,29) , the brain region is “right middle frontal gyrus”.
The Version AFNI_19.0.25 ‘Tiberius’ in lin
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Dan
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AFNI Message Board
Hi, Paul-
In my QC*/index.html output, the "pre-steady state warnings" is none, and I didn't find other warning messages (a screenshot is attached).
best,
Dan
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Dan
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AFNI Message Board
Hi, peter
I'm sorry for the continuous post on the message board, and thank you very much for your patience and help, I might have found out why the ventricle is lit up.
I think the cause of the bright ventricle is that the story time points include the fixation time before the audio was played(8TR fixation time before each story).
The ventricles looks normal when I did the correlation
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Dan
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AFNI Message Board
Hi, peter
1) What's different between your acquisition and that of your colleague?
My colleague's experiment was watching movies and my experiment was purely auditory. We all use a few minutes of natural stimulation, our data analysis methods are the same (do correlation). We were surprised by the bright ventricles, which my colleague's experiment did not show.
2) Have y
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Dan
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AFNI Message Board
Hi,
I have a problem that has been bothering me for a long time, we have been trying to find out why, but nothing.
In our experiment, the subjects are instructed to listen to two four-minute stories(one story, one run), and we want to make the correlation of two runs. But we found the ventricles lit up after correlation(a screenshot in attach file), does anyone have the same problem as me?
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Dan
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AFNI Message Board
Hi,
Is there anyone here who does continuous natural stimulation(auditory)? I am deeply troubled by the results of my experiment.
I have a problem that has been bothering me for a long time, we have been trying to find out why, but nothing.
In our experiment, the subjects are instructed to listen to two four-minute stories(one story, one run), and we want to make the correlation of two r
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Dan
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AFNI Message Board
Hi, ptaylor-
Thank you for your patience! I'm a freshman in fMRI and may often ask some silly questions! The APQC helped me a lot in checking the data.
Thanks again for your generous help!
--Dan
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Dan
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AFNI Message Board
Hi rick,
Thanks for your help, I will check the timing file and other possibilities you mentioned.
Dan
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Dan
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AFNI Message Board
Hi rick,
Thanks for your help ! And I think using "-regress_apply_mot_types demean deriv" is better for my experiment with your help.
Thanks again for your generous help!
Dan
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Dan
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AFNI Message Board
Hi,
My experiment is a ROI localization experiment. In the quality control file generated by afni_proc.py, I don't understand what's the meaning of " check : statistics vol " in the qc file. Can someone explain it to me in detail ? Or where can I find more detail about qc? Attached to this post is a screenshot, which is called "image1"
And I also want to know
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Dan
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AFNI Message Board
Hi rick,
Thanks again for your help. I still have two questions for you, which may seem silly.
First, you mentioned that " Using 'basic' and 'demean' should lead to the exact same results, except for the polort 0 terms ".
1) In the proc file generated by proc.py, I don't know whether the ' polort 0 ' you mentioned is in " running the re
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Dan
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AFNI Message Board
Hi,
I am confused on how to setup the afni_proc.py script to analyze my fMRI task about listening to story. In my experiment, the subjects are instructed to listen to two four-minute stories(one story, one run), and I want to make the correlation of two runs. But I encountered some problems in afni_proc.py script. This is my script:
afni_proc.py -subj_id sub9.c.demean.blur6
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Dan
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AFNI Message Board
Hi rick ,
First, I did a face fusiform gyrus localization experiment,using faces minus houses, we got a fusiform area that was sensitive to faces, but I don't know why can't get the percent signal change of FFA in the subject as my expect.
I've checked the result and it may have nothing to do with the visual cortex.(Please see the image attach file)
And I also provided a QC
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Dan
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AFNI Message Board
I checked the alignment of the EPI and T1 images and the brain masking, the results are in attach files. It's no problem.
And in this sample data, I did not get the ROI percent signal change I expected. It's very confusing.
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Dan
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AFNI Message Board
Hi,
I am running through an analysis with afni_proc.py and getting a problem with one subject that I run. The afni_proc.py command is the following:
afni_proc.py -subj_id sub10_ffa \
-dsets FFArun*+orig.HEAD \
-blocks despike tshift align tlrc volreg blur mask scale regress \
-copy_anat anat+orig
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Dan
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AFNI Message Board
Hey,
When I use afni_prov.py to analyze my data,I am hitting an error with it. Seeing the following in my terminal window:
apqc_make_tcsh.py -review_style basic -subj_dir . -uvar_json out.ss_review_uvars.json
File "/home/menglab/abin/apqc_make_tcsh.py", line 84,in<module>
with open(iopts.json,‘r’) as fff:
IOError: No such file or directory:'out.ss_review_uvars.js
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Dan
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AFNI Message Board