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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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Hello Rick,
So you're saying that I should change the -tlrc_base in afni_proc.py to match the same template that was used in SSwarper like the following?
afni_proc.py -subj_id SSwarpedSubject \
-blocks despike tshift align tlrc volreg blur mask \
scale regress \
-copy_anat
by
Nshin96
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AFNI Message Board
It's been awhile and I thought I'd update my progress and findings.
I've been looking at other scripts and programs and decided to use @SSwarper to perform nonlinear alignment and skullstrip T1 to standard MNI space.
@SSwarper \
-input $subj_id \
-base ~/abin/MNI152_2009_template_SSW.nii.gz \
-subid SSW$subj_id \
I've selected 6 brains (2 control, 1 mild cognit
by
Nshin96
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AFNI Message Board
I suppose, technically, the skull has been stripped? But most of the brain was stripped along with it (and distorted it somewhat), so it doesn't align with the epi data at all. I at least confirmed that the vr_base does align the original anat (before junk) pretty well. I've attached the _al_junk file and the _al_junk file overlayed with vr_base. I've also used "uber_skel"
by
Nshin96
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AFNI Message Board
I've tried 3dTcorr1D (and 3dfim+) and it looks like it works, but I'm not sure if what I am doing is correct. Below is my script so far:
whereami -mask_atlas_Region TT_Daemon:left:precuneus -prefix Lprec
3dWarp -prefix L_precunn -tta2mni Lprec+tlrc
3dresample -master errts.subj.fanaticor+tlrc. -inset Lprecunn+tlrc -prefix L_precuneusM
3dmaskave -mask L_precuneusM+tlrc -quiet errts
by
Nshin96
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AFNI Message Board
Hello, I'm also trying to solve the same problem.
I want to compute the correlation between the seed region (ROI) and the rest of the brain. I'll start with how I created my ROI.
First I created a mask of the left precuneus using the TT_Daemon atlas. Then I warped it to MNI space using 3dWarp.
whereami -mask_atlas_Region TT_Daemon:left:precuneus -prefix Lprec
3dWarp -prefix L_
by
Nshin96
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AFNI Message Board
I've had this problem before. I eventually ended up manually deleting all my R folders and files (because there were old versions of R mixed with new versions of R). Then I re-installed the R-base-core and the AFNI packages to get it to work. But you should try this as your last resort.
by
Nshin96
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AFNI Message Board
As you suspected, I received this output:
ERROR: only Tstats and FStats for now...Sorry!
I'll experiment with tscores in the meantime.
Thanks for your time!
by
Nshin96
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AFNI Message Board
Hello,
I have been having issues with the alignment for some of my data (resting state rsfMRI to T1). It appears that this occurs once every 11 subjects, which is not ideal. A colleague has checked with SPM12 and found no issues on their end. Checking with afni (pb03....volreg file) and QC (attached the files: ve2a.jpg and ve2a_2.jpg for visual), it shows that the problem occurs after tcat and
by
Nshin96
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AFNI Message Board
Hello,
I'm having trouble running ClustExp_StatParse.py.
The below is my code.
ClustExp_StatParse.py -StatDSET stats.ttest+tlrc. -MeanBrik 0 -ThreshBrik 0 -SubjDSET All_clust+tlrc. -SubjTable header_was_the_problem.csv -master ~/abin/MNI_avg152T1+tlrc.
And this is the output.
Resampling master to subject data.
-- will fix any bad char check errors in /data2/open_data/ADNI/AD
by
Nshin96
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AFNI Message Board
As you have suspected, the EPI data evidently had a significant amount of motion. I suppose I shouldn't take all data from ADNI for granted and make sure to double-check everything. I'll keep your advice in mind for future processing.
Thank you again for the help!
by
Nshin96
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AFNI Message Board
Thank you so much for the simple explanation!
For now, I have edited my afni_proc.py based on example 9b: resting state analysis with ANATICOR, as follows:
afni_proc.py -subj_id $subj \
-script proc.$subj -scr_overwrite \
-blocks despike tshift align tlrc volreg blur mask regress \
-copy_anat $top_d
by
Nshin96
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AFNI Message Board
Hello AFNI beginner here,
I have been trying to use uber_subject.py to create an afni_proc.py script to analyze resting state fMRI data of an ADNI subject and received the following error:
[7m** FATAL ERROR:[0m 3dAllineate fails :: base image has 0 nonzero voxels (< 100)
And here are my 3dinfo of the dataset:
3dinfo ADNI_127_S_1427_MR_Accelerated
_Sagittal_IR-FSPGR__br_raw_201
by
Nshin96
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AFNI Message Board