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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,
Although you said "3dTcat is the only AFNI program that will
accept a dataset wildcard along with sub-brick
selectors." But your command doesn't work. Here's the error message.
3dTcat -prefix out_data_filename.nii subj.*.results/stats.*.HEAD[35]'
by
zhenganglu
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AFNI Message Board
Hi,
I have being trying to make 3dLSS work for the past couple of days with no success. In Mumford (2012) paper, they suggested using a Least Square Separate approach, in which you estimate beta separately for each trial of interest with all the other trials as the other regressor.
I have an experiment in which 32 experimental conditions were presented twice in one run and 6 runs in total
by
zhenganglu
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AFNI Message Board
Hi AFNI experts,
I want to use 3dLSS after using afni_proc.py. Is there a way to do this directly through afni_proc or how can I edit the 3dDeconvolve generated by afni_proc.py to be able to use 3dLSS afterwards? The following is generated by afni_proc.py. Thank you so much!
3dDeconvolve -input pb04.$subj.r*.scale+orig.HEAD \
-censor censor_${subj}_combined_
by
zhenganglu
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AFNI Message Board
Thank you so much Cesar! I did include -num_stimts 2 in my 3dDeconvovle. But if you are saying I just need 1 glm with 64 regressors of interests, shouldn't I change it to -num_stimts 64 instead of 2?
Thank you!
by
zhenganglu
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AFNI Message Board
Hi AFNI Guru,
I used a fast event related experiment design and showed 64 images in each run, and in total there were 6 runs. I have come across the paper by Mumford (2012) when I searching the best way to evaluate beta values for each of my 64 images. In the paper, they suggested using a LSS, which could be handled by 3dDeconvolve + 3dLSS. I have read the help for 3dLSS and searched in the fo
by
zhenganglu
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AFNI Message Board
Hi AFNI gurus,
I have to use some mask.nii created by SPM for the beta maps created by AFNI. When I use 3dinfo mask.nii, it shows mask.nii is in ORIG space. I do know that these mask.nii are in MNI space. My thought is, as long as they are in the same common space, I should be fine. Can I just align my stats.nii from afni_proc.py to TT_EPI.nii template?
Thank you as always!
Best,
Z
by
zhenganglu
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AFNI Message Board
Hi,
I understand that --stim_times_IM will give beta value for each stimulus trial. But what if I want beta for each condition per run and do a leave-one-run-out cross-validation? Let's say I have 6 runs scanning, in each run, I have 5 categories with 12 exemplars each, 60 stimuli in total. What if I want to get beta values of the 5 category in each run, instead of 60 betas in each run. I
by
zhenganglu
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AFNI Message Board
Thank you so much! That's extremely helpful! But I'm not familiar with 3dCM. I am reading the Output of -help. I think it should be something like this?
3dCM INPUT
Thank you!
by
zhenganglu
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AFNI Message Board
Hi AFNI masters,
Is there any way I can divided an ROI mask into half and half along y axis. This ROI mask was previously defined using cluster method in AFNI from functional localizer scans.
Thank you so much!
Zhen
by
zhenganglu
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AFNI Message Board
Thank you! I did have a align step in my afin_proc.py. But it keeps giving me WARNING in the terminal...
by
zhenganglu
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AFNI Message Board
Hi all,
I have a quick question. If I aligned the brain along ac-pc during scanning, should I use 3dwarp -deoblique on the anatomical scan before I us afni_proc.py?
Thank you so much!
Z
by
zhenganglu
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AFNI Message Board
Hi Rick,
But gen_ss_review_scripts.py -help_fields doesn't work.
I'm trying to figure out what all these output mean in terms of data quality check.
Thanks!
by
zhenganglu
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AFNI Message Board
Hi AFNI gurus,
Where can I find an anatomical mask for Superior temporal sulcus?
Thank you!
by
zhenganglu
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AFNI Message Board
Hi AFNI and SUMA gurus,
I have functional localized FFA and PPA ROI masks made in AFNI. I have been through freesurfer and SUMA to get the surface ready. I have mapped the volume ROI masks onto surface using ave and max method with 3dVol2Surf. However, the result surface ROI masks look strange in a way that the volume ROI masks have the same voxels size, say 100 voxels, but on the surface the
by
zhenganglu
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AFNI Message Board
Hi AFNI experts,
I am using afni_proc.py to do preprocessing for a two-session experiment. I add the -regress_censor_motion and -regress_censor_outliers options in my afni_proc.py file for each session. Then align preprocessed EPIs from each session to a mean anatomical. After all of these procedures, I put all of the EPIs from 2 session together and did 3dDeconvolve with -regress_censor_motio
by
zhenganglu
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AFNI Message Board
Hi all,
The cross hair label is always in the top of the viewer(e.g. "undefined" if xhair in AFNI goes to the wrong hemisphere). How could I get rid of this label so that only the surface is shown in the viewer window.
Thanks!
by
zhenganglu
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AFNI Message Board
I deleted the space and 3dresample works fine. But how could I continue to finish the rest of steps?
Thanks
by
zhenganglu
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AFNI Message Board