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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
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Thank you for the clarification. I will model each state with the covariates separately.
Thanks,
Tim
by
TimMeeker
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AFNI Message Board
Hi,
I am using 3dttest++ to conduct a paired t-test on two within subjects datasets. Additionally, I want to correlate pain-ratings between two states (with pain and without pain) with the imaging data. However, I get no results when I look at the covariate results. I am not sure how to fix this could I get some advice if this is the proper set of commands.
Thanks,
Tim
Text of Covariates
by
TimMeeker
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AFNI Message Board
Hi Rick,
I've attached the X.xmat.1D file and the output of wc -c `which 3dTproject` is
4399792 /usr/local/AFNI/abin/3dTproject
Thanks,
Tim
by
TimMeeker
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AFNI Message Board
Hi Rick,
That largely fixed it. However it is necessary to change the assumed +orig suffixes on the BRIK files after 3dAllineate in the script to +tlrc suffixes.
Thanks,
Tim
by
TimMeeker
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AFNI Message Board
Hi Rick,
Version AFNI_2011_12_21_1014
[]
Sorry and thanks again,
Tim
by
TimMeeker
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AFNI Message Board
Hi Rick,
No I keep getting the error. I'm running Ubuntu 10.04 LTS - the Lucid Lynx and afni Version AFNI_2011_12_21_1014. This dataset is 1.75 X 1.75 X 4 with 194 TRs though. Also, the alff version (without motion and outlier censoring) runs without any problem.
Tim
by
TimMeeker
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AFNI Message Board
Hi Rick,
I'll try your suggestions. Thanks,
Yeah I've processed this dataset before and it has a lot of motion. The outlier frac does remove about 20% of the data on a few runs in a few subjects. Normally I use 1.0 for regress_censor_motion. I'm using this analysis for a functional localizer so it should be OK.
Thanks,
Tim
by
TimMeeker
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AFNI Message Board
Hello all,
I've been recieving the following error
3dTproject -polort 0 -input pb03.pp004s1R1woWMCSF.r01.blur+tlrc.HEAD -mask mask_group+tlrc -censor censor_pp004s1R1woWMCSF_combined_2.1D -cenmode ZERO -ort X.nocensor.xmat.1D -prefix errts.pp004s1R1woWMCSF.tproject
3dTproject: malloc.c:3096: sYSMALLOc: Assertion `(old_top == (((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2]))
by
TimMeeker
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AFNI Message Board
Hello all,
I have a simple question. I'm running the following afni_proc.py routine:
afni_proc.py -subj_id $subject-$phase-msit -dsets $subject-$phase-MSIT1+orig $subject-$phase-MSIT2+orig -copy_anat $subject-$phase-t1mprage+orig -blocks despike align tlrc volreg mask blur scale regress -move_preproc_files -tcat_remove_first_trs 4 -anat_has_skull yes -volreg_align_e2a -volreg_tlrc_warp -
by
TimMeeker
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AFNI Message Board
Hi Rick,
Thanks for your help. I'm not sure why applying multiple rows to the timing files eluded me. Do they need separate labels or identifiers of any sort or should they simply be in the same order as the files are in the -dset specification?
Thanks,
Tim
by
TimMeeker
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AFNI Message Board
Hello,
I have a block task-based design where each subject performed the same 9 tasks during two seperate fMRI scans within the same session visit. However, the two scans are counter-balanced and have a different order of tasks performed.
For example:
1st scan task order: A-B-C-C-B-A-A-C-B
2nd scan task order: C-B-A-A-B-C-C-A-B
How would I specify two different sets of timing files
by
TimMeeker
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AFNI Message Board
Hello All,
I am having an issue using SurfClust. I do not know what surface filename would put after -surf_A. I did an analysis on surface data and generated a .gii file from 3dANOVA2. I used the fsaverage to normalize the T1mprage files to, but now I'm not sure what input I should set for -surf_A.
SurfClust -spec fsaverage_lh.spec -surf_A -input ANOVALhemimencycthick.gii 1 -rmm 2 -thre
by
TimMeeker
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AFNI Message Board
Hi Peter,
Thanks again. It was the opening dialog box. it would only detect .dset files so I just was able to type in the resulting ANOVA file name and it opened just fine.
Best,
Tim
by
TimMeeker
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AFNI Message Board
Hi Peter,
Thanks again for your help. I am still running into issues as I cannot seem to open the .gii file generated as a -bucket file from the 3dANOVA in suma. Do I need to convert it first or am I missing a fundamental command to view gii files on the fsaverage I generated?
Thanks,
Tim
by
TimMeeker
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AFNI Message Board
It turns out I have a related follow-up question. I just started using suma this last week. How would I make the average volume spec file to load the results onto? What files in the fsaverage directory should I use?
Thanks,
Tim
by
TimMeeker
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AFNI Message Board
Rick and Peter,
Thank you both. I'm happy to see the results are replicable between SUMA and Freesurfer.
Tim
by
TimMeeker
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AFNI Message Board
Hello AFNI/SUMA gurus!
I wanted to know if there was a suggested or validated way to use a combination of suma and afni (with assistance from R perhaps) to conduct a cortical thickness analysis of Freesurfer derived segmentations yielding vertex-wise cortical thickness. My specific problem is that I want to conduct a vertex-wise RM-ANOVA on cortical thicknesses and neither Freesurfer's long
by
TimMeeker
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AFNI Message Board