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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
Page 5 of 5
Pages: 12345
Results 121 - 145 of 145
Hi everybody,
Does 3dMean not handle the filelist: style of command line argument?
3dMean -prefix /Users/colmconn/mriAnalyses/MDD/data/Group.results/sgAccAverage2 filelist:/Users/colmconn/mriAnalyses/MDD/data/Group.results/sgACC.bucketFileList.txt
produces a bucket file with 60 subbriks (the bucket list file contains 60 lines) whereas
3dMean -prefix ~/mriAnalyses/MDD/data/Group.resu
by
Colm Connolly
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AFNI Message Board
That does exactly what I was looking for. Thanks Ziad.
by
Colm Connolly
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AFNI Message Board
Hi,
Is there a way to tell AFNI to use particular LUT for the colors for cluster ordered file (i.e. files resulting from 3dmerge -1clust_* or 3dclust -savemask) by default. Right now when I swap between these the color map is always reset to the red to blue spectrum and I always have to re-chose my desired LUT. What I'm thinking is that it would be useful to be able to say
3dclust -sa
by
Colm Connolly
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AFNI Message Board
I've had no problems with it so far, but I'm only using it to view images on my laptop, nothing very computationally intensive. I, however, use Macports instead of fink so I've found it easier to compile it myself periodically. This gets me around the myriad of library problems that can arrise if you try to use Macports, Xquartz, and AFNI.
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Colm Connolly
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AFNI Message Board
Hi everybody,
I'm running 3dClustSim to get the minimal cluster size for some analyses. I'd like an athr of 0.0125 (0.05/4) but the report produced by 3dClustSim list 0.013 for the athr. I know in the grand scheme of things that 0.005 may not make a huge difference, but I'd still like to know whether 3dClustSim is rounding the 0.0125 to 0.013 in the output or rounding it to 0.01
by
Colm Connolly
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AFNI Message Board
Hi,
Would it be possible to have a link added to the download page for MAC OS X 10.7 (Lion)? Currently it stops at Snow Leopard and the only way to get the tarball is to look under Download all software.
On a related note, have you guys started using AFNI under Mountain Lion? Do you think prebuilt binaries will be available for it soon?
Thanks,
Colm.
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Colm Connolly
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AFNI Message Board
true, but you can still exhaust the length of the command line argument using this method, especially if you include the fill pathname (as I do) for each file.
by
Colm Connolly
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AFNI Message Board
Hi Ziad,
Nope I don't have an attach file link anywhere on my message views
I just uploaded the SUMA directory I created by running @SUMA_Make_Spec_FS. It's called SUMA.for.Ziad.tar.gz. It contains the MNI152 that went into the freesurfer directory. it's called original.MNI152_T1_1mm.nii.gz
There is also a misalignment.png file showing how the stats images (in the ttest.m
by
Colm Connolly
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AFNI Message Board
If you've not heard of GNU parallel you should check it out. It will make splitting your skull stripping across multiple cores easy
by
Colm Connolly
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AFNI Message Board
Hi everybody,
I've generated some surfaces using freesurfer for the MNI152_T1_1mm brain included in FSL and run @SUMA_Make_Spec_FS -sid mni152_T1_1mm in the freesurfer subject which generated a SUMA directory for me.
(I'm using the MNI152 brain because the registration to standard space was done with FLIRT & FNIRT.)
When I try to overlay some stat data that has been regist
by
Colm Connolly
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AFNI Message Board
Thanks, Gang, I'd not seen that paper. It helps immensely as I thought I was going to have to throw out the overlap results.
by
Colm Connolly
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AFNI Message Board
Hi everybody,
I've got a question regarding correction for multiple comparisons in the overlap of clusters derived from LME and separately from robust regressions.
Briefly, I've performed some voxelwise LMEs (in R) on task related GLTs produced by 3dDeconvolve. The model was looking at the effect of group, so the R fixed effects model formula was fmri ~ group. There are 2 groups
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Colm Connolly
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AFNI Message Board
bumping the thread to see if you've given any thought to these requests.
by
Colm Connolly
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AFNI Message Board
I just figured it out. It appears that this subject was heavily censored and the first several volumes in the errts were all zeros, so I thought that something was wrong. I also ran 3dhistog on it and it complained that all the voxels were zero, but it was not processing more than one subbrik. Anyway problem solved with the errts, sorry for the noise.
I've looked through the output of gen
by
Colm Connolly
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AFNI Message Board
3dDeconvolve complains about nothing.
I was trying to run gen_ss_review_scripts.py (which I assume generates @ss_review_driver) as follows but it doesn't complete.
Note that I do not use afin_proc.py to do the preprocessing of the data as I do that with my own scripts that process the anatomy and EPI data nonlinearly into MNI space.
> gen_ss_review_scripts.py -subj 330_A -tcat_d
by
Colm Connolly
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AFNI Message Board
Hi everybody,
I'm using 3dDeconvolve to clean up some EPI data for resting state analyses. I'm using example 9 from the output of afni_proc.py as my guide and am running 3dDeconvolve indicated below. The problem I'm having is that my errts timeseries is entirely zero. Can any one see any problem with my command that might give rise to this issue?
subjectNumber=330_A
prefixPr
by
Colm Connolly
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AFNI Message Board
Ok So I found the crash report hidden in Library/Logs/DiagnosticReports in case it is of use.
Process: 3dAllineate [31884]
Path: /Users/USER/*/3dAllineate
Identifier: 3dAllineate
Version: ??? (???)
Code Type: X86-64 (Native)
Parent Process: tcsh [31882]
Date/Time: 2012-07-09 14:48:47.260 -0700
OS Version: Mac OS X 10.7.4 (11E53)
Repor
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Colm Connolly
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AFNI Message Board
Hi everybody,
I'm having trouble getting 3dAllineate (called via align_epi_anat.py) to complete: it's continually terminating with an Abort.
I call align_epi_anat.py as follows
align_epi_anat.py -anat 330_A.anat_struc_brain.std+orig.HEAD -anat_has_skull no -epi_strip 3dAutomask -epi 330_A.restingstate.std+orig.HEAD -epi_base 0 -epi2anat
which does it's thing and then ca
by
Colm Connolly
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AFNI Message Board
I'd suggest the -filelist myfiles.txt format to minimize the problem with yet another special syntax.
I suggested the - to keep it similar to 3dUnDump. This example is cut'n'pasted from the 3dUndump help
3dROIstats -mask mmm+orig -1Dformat func+orig'[1]' | \
| 1dcat stdin: | 3dUndump -prefix uuu -datum float -ROImask mmm+orig -
BTW, I'
by
Colm Connolly
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AFNI Message Board
The problem with this is that it's possible to overrun the command line limit. I've tried it and done it as I include full pathnames to files to eliminate any ambiguity.
by
Colm Connolly
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AFNI Message Board
Hi everybody,
I've got two feature requests that I'd like to ask for:
1. 3dbucket: Could it be augmented so that if a - is provided on the command line that it would read the list of files to go into the bucket from standard input rather than from the command line itself? That is cat listOfFilesToPutInBucket.txt | 3dbucket -fbuc -aglueto $groupResults/$task.$groups.outcome+tlrc -
by
Colm Connolly
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AFNI Message Board
If I've understood you correctly and you want a count of the number of occurrences of 1, 2, 3, ..., 10, etc then 3dhistog will give you what you want
For example, with a mask file containing 2 ROIs numbered 1 and 2 I get the following from 3dhistog:
++ 3dhistog: AFNI version=AFNI_2011_12_21_1014 (May 25 2012) [64-bit]
#Magnitude Freq Cum_Freq
0 90022
by
Colm Connolly
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AFNI Message Board
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