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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 gurus -
Is there a way to implement the Clustering GUI's new bi-sided capability with 3dclust? Is that coming?
Thanks!
JP
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JoshPowell
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AFNI Message Board
Hi all-
I'm getting some crashes with plugout_drive, for example:
% plugout_drive -npb 1 \
-com "SWITCH_UNDERLAY TT_N27" \
-quit
? -com "SWITCH_UNDERLAY TT_N27" \
? -quit
PO: plugout connection from host 127.0.0.1 (tcp:*:1057)
PO: plugout connection name is ManOfLaMancha
Fatal Signal 11 (SIGSEGV) received
CLU_setup_alpha_tables
by
JoshPowell
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AFNI Message Board
Hi all-
I've been wrestling with this code for quite awhile, to no avail, and need a clear head. I'm frustrated, because it's such a simple thing that I *know* (think, hope...) has worked in dozens of previous scripts.
This does not work:
3droistats -mask mymask+tlrc `cat 3droistats_dset_list` > roistats_output.txt
It returns:
Warning: Cannot open input dataset &
by
JoshPowell
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AFNI Message Board
Congratulations and thanks for this!
I have some colleagues who are very interested, and I think I expressed that, but then succumbed to the eternal curse of too much to do. Sigh.
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JoshPowell
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AFNI Message Board
Hi Sarah-
You want to use the "Resamp" "ULay" button in the "Define Datamode" pane on the AFNI controller. The process is described in a bit more detail in handout # 10 on Volume Registration/Talairach Transformation (http://afni.nimh.nih.gov/afni/doc/edu/afni10_volreg_talairach)
Cheers,
Josh
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JoshPowell
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AFNI Message Board
Hi Jadrana-
I think this command will get you the motion plot you're looking for:
1dplot -volreg -one -xlabel TR -ylabel mm dfile.rall.1D
We use a script which includes features for customizing axes, marking multiple runs, and including more information in the window title. I could send that if you like - just email me, or send a PM with your email address. Seems I can only attach ima
by
JoshPowell
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AFNI Message Board
Thanks Daniel. I did a quick test and it looks like recentering and giant_move may work, but I may need some zeropadding as well to prevent cutting the anatomical. I'll post back when I find something that works well and limits transformations.
JP
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JoshPowell
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AFNI Message Board
Thanks Daniel, for your reply. I spent some time playing with -master_anat, but without much luck.
Option A seems to give about the same result as what I had - anatomical data cut-off in the same way EPI is (intentionally) cut off. Data definitely then needs to be shifted before running @auto_tlrc...that output suggests @Align_Centers, which works fine, but I'm guessing I'll need to
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JoshPowell
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AFNI Message Board
Hi Rick (et al)-
We've found that we have to deoblique both functional and anatomic data, and typically add those steps to scripts produced by afni_proc.py. I've tried various approaches to skip this (including the two you just suggested) without much luck.
For example, these commands lead to truncated anat data, matching our EPI, which doesn't acquire some of the parietal lo
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JoshPowell
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AFNI Message Board
Hi all-
I'm getting the following error when trying to post a reply (Preview or Post Message) on the message board:
Forbidden
You don't have permission to access /afni/community/board/posting.php on this server.
JP
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JoshPowell
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AFNI Message Board
Hi gurus-
We've got some @auto_tlrc failures, due to pretty bad anatomical scans, that we've decided to manually transform (following the instructions in afni10_volreg_talairach.pdf Appendix C. We then would like to feed that data into the existing processing script where the @auto_tlrc transformation would be applied to follower datasets. The command is:
@auto_tlrc -onewarp -ap
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JoshPowell
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AFNI Message Board
Thanks Rick! Yep, /usr/local/afni/bin and ~/abin. Out of curiosity, is there a way for a user to keep a ~/abin? (If for some reason they want to use a different version than everyone else is using.) I guess they'd have to replace /usr/local... with ~/abin, rather than just appending ~/abin to the PATH.
Cheers,
JP
by
JoshPowell
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AFNI Message Board
Hi all-
Our group is getting the following error message shortly after starting AFNI on one of our iMacs; specifically after opening a few datasets and working for 1-2 minutes. Seems to be isolated to one iMac. We've re-downloaded AFNI binaries but the message persists. I'm thinking there's a conflict with the OS or X11, but would like to have some expert input before I start r
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JoshPowell
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AFNI Message Board
Hi Guillaume-
I think you can also include subjects with visible motion artifacts, as long as you censor the TRs affected (or confirm that AFNI is censoring them automatically.) We create a list of artifact timepoints to censor when doing @epi_review. Usually it's only 1-3 TR's, and only with extreme motion (>1mm, roughly.) I'm always curious to hear what other labs are do
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JoshPowell
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AFNI Message Board
Hi all-
This is slightly off-topic, but certainly related to things AFNI. Does anyone have a recommended external storage system for about 10TB of data? Could be direct-attached storage (DAS) or network-attached storage (NAS). I'm specifically hoping to use it for Apple Time Machine backups of our primary analysis workstation, which currently has about 7TB of data. We have used a coup
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JoshPowell
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AFNI Message Board
Good to know, thanks Rick! Would you be willing to add this warning to the automask section of the 3dFWHMx help file? Since it's recommended to use residuals as input, it's easy to imagine that other users might make this mistake.
Thanks again,
Josh
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JoshPowell
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AFNI Message Board
Hi Rick-
Thanks! Seems like -automask should (and in one trial, does) take care of this.
JP
by
JoshPowell
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AFNI Message Board
Hi Rick et al-
I've had a similar problem with 3dFWHMx underestimating smoothness. In my case, it seems to happen only when I use the 'detrend' option. I'm not sure whether this is a bug with detrend, or perhaps detrend is inappropriate when using data that doesn't have anatomical detail (i.e. residuals.)
Here's example output, and I'll upload some data m
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JoshPowell
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AFNI Message Board