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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
This comes up from time to time. The answer is currently "no, you can't run clusterize from the plugout_drive". That said, you could run 3dclust or 3dmerge on your data, and display that output of those tools in the AFNI viewer using plugout_drive to set the appropriate p-value threshold.
Previous Threads:
by
Peter Molfese
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AFNI Message Board
Have you tried overlaying the output of 3dAllineate on the TT_N27+tlrc brain? If this registration is significantly off, then I would suspect the output of 3dQwarp would also be incorrect.
I would suggest mimicking how afni_proc.py performs the warps via auto_warp.py, which will perform the affine transform (via @auto_tlrc) and then 3dQwarp. Your 3dNwarpApply command looks correct. You cou
by
Peter Molfese
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AFNI Message Board
To remove the values of -1 from your mask, you can do something like:
3dcalc -a yourdataset.nii.gz -prefix yourOutputMask.nii.gz -expr 'equals(a,1)'
by
Peter Molfese
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AFNI Message Board
Kausar,
Can you post the commands you are using. 3dQwarp has been working well for my data. Also what version of the binaries are you running?
-Peter
by
Peter Molfese
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AFNI Message Board
That's unusual. Can you tell us more about the command you are running?
Also, what is the output of:
afni -ver
And if you are running a recent build of AFNI, the output of:
afni_system_check.py -check_all
by
Peter Molfese
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AFNI Message Board
If you have an equal number of subjects in each cell of the design, then 3dANOVA3 should work fine. If you have an unbalanced design, or you have covariates, you can fit your model with 3dMVM.
by
Peter Molfese
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AFNI Message Board
I suspect it's causing an error due to what comes directly after the task contrast. In your lines:
-gltLabel 4 CON_PDL_same_vis -gltCode 4 'task : 1*same_vis : 1*CON_1 -1*PDL_1' \
-gltLabel 5 CON_PDL_same_nv -gltCode 5 'task : 1*same_nv : 1*CON_1 -1*PDL_1' \
You are missing the variable name preceding the Group part of the contrasts. Try:
-gltLabel 4 CON_P
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Peter Molfese
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AFNI Message Board
Did you install the necessary packages inside of R?
install.packages("afex")
install.packages("phia")
install.packages("snow")
Alternatively do all three in one:
install.packages( c("afex", "phia", "snow"), depend=T)
by
Peter Molfese
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AFNI Message Board
It looks like you do not have R installed. If this is the case, you should get a copy from CRAN.
by
Peter Molfese
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AFNI Message Board
If you run @SUMA_Make_Spec_FS on all of your Freesurfer folders, you can then take the SUMA folder contents (particularly the aparc+aseg_rank.nii) and use that to identify anatomical regions to pull out activations via a mask. I would probably use 3dcalc to do this for each subject. An example of pulling out the left putamen might go like this:
3dcalc -a 'subj001/SUMA/aparc+aseg_rank.
by
Peter Molfese
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AFNI Message Board
It sounds like you have at least one subject with a different dimension image. In the folder that you have all of your data files try the following:
3dinfo -header_line -prefix -d3 -n4 *.HEAD
Which will output the dataset name, three values depicting voxel dimensions, 3 depicting grid size. Adding -same_grid to the command will add a column testing if the datasets are on the same grid.
by
Peter Molfese
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AFNI Message Board
Hmm. I see it in my distribution - macosx_10.7_Intel_64: Aug 27 2013. Perhaps you need to update your binaries? What's the output of afni --version?
by
Peter Molfese
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AFNI Message Board
Hi Dane-
3dmaskave is giving an error because it expects the mask to already exist. To create the masked region based on the anatomical atlas, you should use whereami (code snippet below):
whereami -atlas CA_N27_MPM -mask_atlas_region CA_N27_MPM:176 -prefix Area6
This will extract all of Area 6 as an ROI mask. You will then likely need to down sample the mask to match your stats datas
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Peter Molfese
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AFNI Message Board
Hi Adam,
If you wish to do an ANCOVA, you might find 3dttest++ or 3dMVM easier.
If you are absolutely determined to use 3dRegAna, you will need to "dummy code" your task variable. You can see Example 4 in the 3dRegAna white paper for guidance. If you have repeated-measures (i.e. everyone in the experiment did all 4 tasks) then things get even more interesting...
It's
by
Peter Molfese
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AFNI Message Board
I'm guessing that your labmate has Bash (or another shell) as the underlying shell, which is more forgiving about not having quotes around the [ ].
by
Peter Molfese
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AFNI Message Board
I suspect that your underlying shell is tcsh and not bash. If the output (outside of MATLAB) of "echo $SHELL" is /bin/tcsh, I would try adding quotes around the sub-brick selectors (for example: '[3]').
See this thread for a user with a similar issue:
Once you add the quotes around the selector it should work in either the shell directly or via MATLAB's unix com
by
Peter Molfese
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AFNI Message Board
The 10.7 binaries work well for me on 10.8.4 systems. It's good to see the AFNI is working on the path. What error are you getting when you issue the command in MATLAB?
You shouldn't need a compiler or even fink for these commands to work.
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Peter Molfese
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AFNI Message Board
Outside of matlab, what do you get if you type the following commands?
which afni
afni -version
by
Peter Molfese
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AFNI Message Board
N27 Surface are available in both TT and MNI spaces:
TT:
MNI:
by
Peter Molfese
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AFNI Message Board
The Cygwin version hasn't been supported (or updated) in a while. Instead, the current recommendation is to use something like Virtual Box and run the Linux version of AFNI inside of that.
by
Peter Molfese
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AFNI Message Board
Hi Elissa,
Some of the interpretation depends on your model. The F-stat tests the difference between the restricted-model and the full-model. If the difference between those two models is one variable, then the Coef/Tstat map will be the same as the F-stat map, except that the t-stat will show the direction (See: ).
When viewing the data, use the Coefficient and the respective T-stat.
by
Peter Molfese
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AFNI Message Board
Yang,
According to the help 3dNwarpApply allows for applying affine transforms (coming out of @auto_tlrc, align_epi_anat.py or 3dAllineate) with the nonlinear transforms of 3dQwarp. However, FSL's flirt uses a different coordinate system (LPI) than AFNI. So you could try modifying the flirt matrix to match the RAI system that AFNI uses, in which case this thread may be helpful.
I
by
Peter Molfese
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AFNI Message Board
Otto,
Even with a mask, a t-test on only 7 subjects is going to have a hard time finding a large enough set of significant voxels to give you a q-value in the range that you would like. See this thread for similar advice.
As for the 3dClustSim... You need to estimate the smoothness of each of your subjects via 3dFWHMx and then average that smoothness value as your inputs for 3dClustSim.
by
Peter Molfese
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AFNI Message Board
In order to get the p-value for the Report window, you need to use 3drefit to add the Cluster information. There's some information in the help for 3dClustSim (briefly pasted below).
3dClustSim -mask mask+orig -fwhm $fwhm[4] -niml -prefix CStemp
3drefit -atrstring AFNI_CLUSTSIM_NN1 file:CStemp.NN1.niml \
-atrstring AFNI_CLUSTSIM_MASK file:CStemp.mask \
by
Peter Molfese
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AFNI Message Board
You're running into problems due to the block of code below, which expects to find the template in either the AFNI directory or on one of the AFNI-specific paths (e.g. AFNI_PLUGINPATH).
set tpath = `@FindAfniDsetPath $basename`
if( $tpath == '' ) then
echo "** @toMNI_Awarp: Failed to find template $basename -- cannot continue"
exit 1
endif
The easiest fix
by
Peter Molfese
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AFNI Message Board
It looks like you have some of your lines mislabeled. Starting with the line below, instead of 1 1 X it should be 1 4 X.
-dset 1 1 1 ~/Desktop/Data/FaceTask/5025/5025.results/stats.5025+tlrc'[19]' \
I make this mistake from time to time. An easy way to check it is to load all of your dset lines into R and then run table on each of your 3 factor columns:
table(thedata[1])
by
Peter Molfese
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AFNI Message Board
Andrew-
It sounds like you have a fairly complex setup (Condition X Time X Group). The easy option is often to specify the linear trend at the single subject level in your 3dDeconvolve step and then take that GLT to your group level analysis in 3dMEMA/3dttest++/etc.
The other option given your design is to use 3dMVM. See the help via 3dMVM -help. 3dMVM will allow you to have multiple f
by
Peter Molfese
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AFNI Message Board
Otto,
It is unclear if 1) you are trying to create the dataset directly on the CD (which will give you a write error) or 2) if your different runs are in different directories. I recommend for the purpose of converting files that you copy the DICOMs to your hard drive. Then if your DICOM files are all in one directory, you will need to sort them into one directory per sequence. Fortunately
by
Peter Molfese
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AFNI Message Board