Show all posts by user
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
Results 2131 - 2160 of 2305
Two minor notes:
1) For 3dTrackID, there is now an option available to *not* output the *INDIMAP* and *PAIRMAP* files. This may be useful in cases where one is doing a connectome-like analysis with maaaany target ROIs. When there are N target ROIs, the INDI and PAIR maps will each have N+1 bricks; in cases of large N (>100, say?), and depending upon computer resources, users may not want
by
ptaylor
-
AFNI Message Board
1) An important default setting in 3dROIMaker is being changed, to bring the program's behavior in line with other AFNI functionality.
Different software packages have different default definitions of a voxel neighborhood. The categories are typically described in terms of what basic features must be shared in order to make two voxels neighbors: nodes, edges or faces. The three main c
by
ptaylor
-
AFNI Message Board
What is the problem with using commandlines in Ubuntu?
As someone who uses AFNI a fair amount on Ubuntu, I would have voted for that platform as pretty straightforward and reliable.
--pt
by
ptaylor
-
AFNI Message Board
I think that, in going through the warping process, your data set has lost its table-- so, probably when you view 'mask_aseg_nl_1.4+tlrc' in an AFNI window, you don't see labeltable functionality on it.
However, I have it on good authority (-> Rick's) that you can reattach it or copy it using 3drefit, with either of the following options:
-labeltable TTT Inset the
by
ptaylor
-
AFNI Message Board
>> do you know off the top of your head the program for selecting just a single row out of a file? sounds like it could just be a general unix thing. no worries if it doesn't pop to mind, i can figure that out
fat_roi_row.py (it's part of AFNI/FATCAT).
>> more importantly, though, what's the syntax for adding a label table? i tried a couple things that didn
by
ptaylor
-
AFNI Message Board
Great, glad things are going well.
>> is there a way to tell 3dNetCorr to ignore some mask values or do i have to change the image mask itself (zeroing out values with 3dcalc for example)?
3dNetcorr will deal with all ROIs, so those would have to be edited out, either before or after running-- for the former, probably 3dcalc'ing, yes; for the latter, Python/matlab trickery to w
by
ptaylor
-
AFNI Message Board
Hi-
First, I would transform the various ROI maps into your EPI space (so, yes, I agree with you, into the 1.4mm space), for example with 3dAllineate.
Then, if all the ROIs are in a single network, I would then combine them into a single volume. If there are multiple networks, you could make each grouping a separate brik in a single file. This can be done using 3dTcat and/or 3dcalc. Proba
by
ptaylor
-
AFNI Message Board
I'll just a couple things to Peter's recommendations.
Yes, the Demo would probably be key to look at for starters-- there are a number of scripts in a ~pipe-liney-type ordering for making networks of target (functional) ROIs, and then for performing different forms of tractography through them. There are comments in the scripts, as well.
And yes, 3dDWUncert gets run before '
by
ptaylor
-
AFNI Message Board
Well, I'll be sure to read the helpfiles more carefully from here on.
Cheers,
pt
by
ptaylor
-
AFNI Message Board
Well, that's embarrassing... The package installations sorted me out. I should have remembered to do that on that machine.
Thanks for the patient assistance, anyways.
Cheers,
pt
by
ptaylor
-
AFNI Message Board
Ugh, sorry, I was in a directory where I had been testing other things...
When I run those commands in the *correct* place, then it pretty much looks like 3dMVM runs as normal, hanging again at:
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++
Reading input files now...
--pt
by
ptaylor
-
AFNI Message Board
Did not make it to Step 3:
> source('~/afni_src/linux_ubuntu_12_64/AFNIio.R')
> load.debug.AFNI.args('.3dMVM.dbg.AFNI.args')
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file '.3dMVM.dbg.AFNI.args', probable reason 'No such fi
by
ptaylor
-
AFNI Message Board
Sure, blame the FATCAT data sets...
Yes, they are FATCAT data sets, 17 ROIs and 60 subjects-- set it running, and it hadn't finished overnight. Even the small FATCAT demo set took a very long time; however, these all took *much* shorter to run on my laptop.
--pt
by
ptaylor
-
AFNI Message Board
Boom! That did it. Thanks very much, Isaac and Peter.
Summary for anyone else in similarly leaking boat:
+ in all Makefiles: 'cc' -> 'gcc'
+ make sure that 'gcc' was not the Apple one, but the newly built one (in this case selecting with macports)
+ purging references to '-no-cpp-precomp' in all Makefiles.
+ (possibly) comment out OMPFLAG
by
ptaylor
-
AFNI Message Board
Hi, Isaac-
I now tried setting the new macport gcc compiler as the selected version, via:
$ sudo port select --set gcc mp-gcc48
so that this happens without any aliasing in the ~/.bashrc:
$ gcc --version
gcc-4 (GCC) 4.8.2
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY o
by
ptaylor
-
AFNI Message Board
Hmm, that lead to the following immediately:
bash-3.2$ sudo make vastness
( cd niml/ ; make all 'CC=gcc -O2 -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -UDONT_USE_MCW_MALLOC ' ; /bin/mv -f *.o .. ; )
clang: error: no such file or directory: '( cd niml/ ; make all 'CC=gcc -O2 -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cp
by
ptaylor
-
AFNI Message Board
bash-3.2$ which gcc
/usr/bin/gcc
bash-3.2$ gcc --version
gcc-4 (GCC) 4.8.2
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
And I note that in my ~/.bashrc file, I made the alias:
alias gcc='gcc-4'
by
ptaylor
-
AFNI Message Board
Hi-
Amongst my recent computer woes, I have had a problem with 3dMVM in particular on my Ubuntu-- the same command/data that runs very quickly on another computer (such as a Mac) takes muuuch more time on a reasonably powerful/large RAM Ubuntu, 14.04. I assume it's something with the R usage, though other programs using R (3.something) haven't been so slow for me.
I have tried
by
ptaylor
-
AFNI Message Board
Also, Peter-
Following what you'd mentioned about difficulties with the Clang compiler, I tried replacing all the 'cc's in the Makefiles (all the ones I could find, at least) with 'gcc', (still using the main 10.6.8-mac Makefile). However, I still got the same error, oddly enough, at the end, :
gcc -O2 -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no
by
ptaylor
-
AFNI Message Board
Hi, Peter-
Thanks, I did an upgrade (not a clean install).
Yes, I downloaded the newest Xcode and the did the commandline tools install. I guess I have to see if some particular linked library is now 'bad' or changed version or something?
I used macports to get gcc48, and aliased that to be my gcc compiler. (Re. fink, which is what I used to use-- I believe that I would have
by
ptaylor
-
AFNI Message Board
... and, as an intermediary question, I would also be happy to know what precompiled binaries people use, as well, for Mac Mavericks.
Cheers,
pt
by
ptaylor
-
AFNI Message Board
Hi-
Recently updated from Mac 10.6.8 to Mac Mavericks (10.9.5). And of course, I'm suffering with some of the changes. I can no longer build from source.
For starters, what makefile should I use to build AFNI from source? I tried various Makefile.macosx_10.{7,8}* without success, getting quick breaks:
bash-3.2$ sudo make vastness
( cd niml/ ; make all 'CC=/usr/local/bin/gcc
by
ptaylor
-
AFNI Message Board
I'm not seeing an attached image, but I can guess you mean either one of two things:
A) an FA map colorized by local direction of first eigenvector (blue, superior-inferior; etc.); or
B) little, tiny overlay lines per voxel showing local orientation of the first eigenvector.
For case (A), see for example using 3dThreetoRGB:
For case (B), this is really a larger AFNI/SUMA-viewi
by
ptaylor
-
AFNI Message Board
Hmm, would you want to send me a problematic set of LIST_ROIs and I could take a look?
While overlap may exist for several other ROIs, the question is whether a couple ROIs get *totally* occluded for some subjects, which appears to be happening here (must be happening in solidarity with the recent lunar eclipse...).
Regarding overlaps/mapping, if you have a single data set with lots of ROIs
by
ptaylor
-
AFNI Message Board
Hi,
Is it possible that some of the ROIs in LIST_ROIs overlap for these subjects, and therefore some are getting 'overwritten' in the 3dTstat -argabsmax1 phase?
I was also wondering why the '-sum' option is there? Does that mean that if two ROIs overlap, their integers would be summed? If so, that could wash out values you don't want. I think I'm not unde
by
ptaylor
-
AFNI Message Board
If the ROI labels are also missing in the *.roi.labs output, then my guess is that those regions are not actually labelled in the network of ROIs file for those subjects. Do those happen to be small regions that might be squeezed out in mapping, or near a boundary?
Your network of targets for tracking looks to be called "${subj}_Masks/${subj}_all_masks+orig." If, for the sake of bre
by
ptaylor
-
AFNI Message Board
Wow, that's very odd, and I'm not sure what's going on with it.
Firstly, can I ask when your compile date for afni is?:
$ afni -ver
Secondly, if you've rerun tracking for a subject where that number misses, is that number still missing?
Thirdly, since you're using the '-write_rois' option, in your *.roi.labs output file for those particular files, are
by
ptaylor
-
AFNI Message Board
That was my understanding heading into this calculation.
I was assuming that I should calculate the -plusminus warping for just the b=0 and then apply it to the cases of each DWI-- would it make sense to map each DWI individually?
One thing I could do as well would be to average the b=0 images and then do this, but I figured it wouldn't make a huge difference to start.
Cheers,
by
ptaylor
-
AFNI Message Board
I think that's a fair summary of how things look. I was a bit suprised that the peripheries were quite different, but as you explain, perhaps that's reasonable to find. I guess these could only be sorted out by using a tertiary reference, such as an anatomical?
Would it make sense to try to map each to an anatomical separately, and then try to glue the results together? Or is that
by
ptaylor
-
AFNI Message Board
Hi,
I am processing some DTI data (4 b=0 and 30 DWIs), which was aquired with AP-PA (->blip down-blip up, respectively). I have processed each blip-set individually for motion+eddy distortion correction in TORTOISE. In terms of gluing them together now, I am trying 3dQwarp -plusminus to do so. I am wondering if what follows is a reasonable way to go:
$ 3dQwarp -base ./dwi_AP_DMC_FSL
by
ptaylor
-
AFNI Message Board