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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
Hi Omar,
I'm glad you found the blog post helpful. Before I get to your question, I just wanted to point out two things. First is that in your 3dcalc -expr, you're essentially setting a threshold (here 0.25) which isn't mandatory, but when I wrote the blog post I was referring to one of Daniel Glen's posts. Second, I have found that using TORTOISE for preprocessing may y
by
Peter Molfese
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AFNI Message Board
Hi Peter,
You can modify the ~/.afnirc file to make the settings stick.
Best,
Peter
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Peter Molfese
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AFNI Message Board
That's odd. I wonder if the way that Apple aliases gcc to clang is causing problems. What is the output of:
which gcc
and
gcc --version
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Peter Molfese
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AFNI Message Board
Hi Paul,
I'm using the macosx_10.7_Intel_64 build with OS X 10.9.5.
On your compile issue, did you do an upgrade or a clean install? Did you download the newest Xcode and install the command line tools? There's an issue getting OpenMP to build with Clang (Apple's C++ compiler), so you may have to grab GCC via either fink or (my preferred method) Homebrew and then if you h
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Peter Molfese
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AFNI Message Board
To fix the 3dfractionize error, you can use 3dcalc to convert a dataset to byte or short format.
3dcalc -byte -prefix AMG_mask_byte \
-a ROImask_BilatAmy+tlrc \
-expr 'a'
The data not ending up in the right place was due to not specifying a warp to go from the standard space mask to the subject space residual data. Providing 3dfractionize with -warp SubjectAnatomical+tlrc wi
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Peter Molfese
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AFNI Message Board
Hi Jessica-
It looks like it's @auto_tlrc that's asking for the -ok_notice to be specified (not afni_proc.py). If you insert -tlrc_opts_at before the -ok_notice, everything should work.
What is the output of "afni -ver"? I have only experienced the warning when trying to use the TT_avg152+tlrc as a template.
Peter
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Peter Molfese
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AFNI Message Board
I'm fairly sure that it's the double interpolation happening in @auto_tlrc. You can try the -onewarp option on your data to see if that helps.
-onewarp : Create follower data with one interpolation
step, instead of two.
This option reduces blurring of the output data.
It is not used by default for backward
compatibility.
My very quick test
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Peter Molfese
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AFNI Message Board
Assuming you want to take one sub-brick of each subject (such as a coefficient in the stats file output by 3dDeconvolve), then 3dTcorr1D can do this. Though you'll have to do some basic legwork to get the files ready. First, put all of your scalar values in one text file (.1D), each column representing a different variable. Then you can use 3dbucket to create a single file with all of the
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Peter Molfese
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AFNI Message Board
To followup on Gang. In your case, the answer is C.
Since each participant is contributing a single value for each voxel, 3dttest++ has no way of knowing that it was a "dead voxel" for a particular participant. I imagine it would be hard to identify a "dead" voxel by the stats files alone going into a group analysis program as 1) zero is a valid number and 2) I suspect
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Peter Molfese
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AFNI Message Board
Lots of possibilities, but I would start with 3dfractionize:
3dfractionize -template grid+orig -input data+tlrc \
-warp anat+tlrc -preserve -clip 0.2 \
-prefix new_data
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Peter Molfese
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AFNI Message Board
+orig is (almost always) referring to data in subject space. I'm not sure why FSL didn't mark the bit in the header to identify the dataset as in standard space, but if you are sure that the data now reside in MNI space, you can use 3drefit to correct the header information:
3drefit -space MNI MyImage.nii
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Peter Molfese
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AFNI Message Board
Hi Hayriye-
Let us know what your align_epi_anat.py syntax is. We might have suggestions!
P
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Peter Molfese
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AFNI Message Board
Hi Hayriye-
You can use 3dresample to change the orientation:
3dresample -orient RPI -inset T1.nii.gz -prefix T1_RPI
You can combine the orient and resample by using the -master option as well (see help page here).
If you wanted to use the AFNI program align_epi_anat.py, there is no need to modify the T1 image to be the same orientation or resolution as the EPI. You could use it t
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Peter Molfese
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AFNI Message Board
Hi Hayriye-
3drefit simply changes the header information, but doesn't actually alter the data. If you just wish to change the voxel size, then you could consider 3dresample's -dxyz option. However if you're planning to coregister/align the EPI data with an anatomical, you might consider using align_epi_anat.py which can both do the alignment and also change the voxel dimensio
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Peter Molfese
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AFNI Message Board
Hi Leslie-
3dANOVA3 can handle multiple groups and repeated measures, see Type 4 and Type 5, it does require you to have a balanced design. If you have unequal participants in each group, or need for a four-way (or higher factor) ANOVA, I would recommend using 3dMVM (Gang's new program) instead of the MATLAB toolbox (GroupAna). Information can be found here and the help page for the pro
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Peter Molfese
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AFNI Message Board
Hi Mahsa,
There's some ambiguity in your question, I usually attribute "original" space to mean subject space. So it is possible to go from Tal to subject space using the inverse transform, easily implemented with 3dfractionize.
3dfractionize -template grid+orig -input data+tlrc \
-warp anat+tlrc -preserve -clip 0.2 \
-prefix new_data
It is also possible to conver
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Peter Molfese
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AFNI Message Board
Your steps look correct. The one thing that I'm not sure you mentioned is that your EPI datasets need to be coregistered/aligned to the anatomical datasets (I usually use align_epi_anat.py to do this). The outcome of this can be verified by looking at each individual's single-subject statistical results on the respective anatomical file. If you use afni_proc.py, it will generate the
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Peter Molfese
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AFNI Message Board
Hi,
Can you give us your entire afni_proc.py script? Is there anything unique about this one subject's anatomy or scan - such as partial coverage? Most other subjects look good after processing?
You can try using uber_align_test.py to try out different cost functions between the EPI and anatomical, once you've found one you can add options to the processing script with the fla
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Peter Molfese
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AFNI Message Board
Hi,
Just a clarification, you said that you were using each subject's mask after warping them to standard space. But your syntax shows that the input files are still in +orig. Even in your 3dinfo statement you have avg_group_mask+orig, which suggests that the masks are not in standard space.
If it's not a typo, then you will need to warp the masks to standard space using @auto
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Peter Molfese
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AFNI Message Board
Hi Matt,
Most programs don't respect the additional AFNI information in the NIFTI header. Since you can write NIFTI files from most AFNI programs, you could break the GLM results up using 3dbucket and some creative looping (in bash here):
for aNumber in 0 2 4 6 8 10
do
3dbucket -prefix glm.$aNumber.nii GLM+orig"[${aNumber}]"
done
You'll need to modify the num
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Peter Molfese
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AFNI Message Board
While Rick is definitely the expert here, I think you need to do the following:
1) Install dependencies necessary to build at all, these vary by your system but on my computer were things like FreeType, Expat, and FontConfig
2) Download AFNI source for your system
3) In afni_src folder, copy the makefile for your system and then rename the copy as just Makefile
4) Build libmri - make libmri
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Peter Molfese
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AFNI Message Board
Postdoctoral position in Cognitive Neuroscience at Haskins Laboratories
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Peter Molfese
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AFNI Message Board
Research Technician position in Cognitive Neuroscience at Haskins Laboratories
Applications are solicited for a Research Technician in Cognitive Neuroscience at Haskins Laboratories. Applicants should have a M.A., M.S., or Ph.D. in psychology, linguistics, cognitive neuroscience, computer science, or a related field. The selected candidate will contribute to multiple funded NIH studies of spee
by
Peter Molfese
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AFNI Message Board
I'm guessing that this thread is moving along the same scope as one of your other threads, where you're trying to use afni_proc.py to do certain things, pause and do registration in FNIRT and then continue on the afni_proc.py script.
If the registration via FNIRT is the only thing happening outside of AFNI tools, one thing you could try is to allow afni_proc.py to generate the enti
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Peter Molfese
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AFNI Message Board
Hi Tim,
Just to make sure, you're getting all of the Left Hemisphere files and running an ANOVA on those and then the same steps for the right hemisphere? You should then have two outputs from 3dANOVA, one being something like lh.bucket.gii and the other being rh.bucket.gii.
Once you open SUMA with the fsaverage_both.spec (or either the fsaverage_lh.spec/fsaverage_right.spec), right
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Peter Molfese
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AFNI Message Board
If you use the method I talked about with mris_convert, then you can use the fsaverage as your spec to overlay results onto.
cd $SUBJECTS_DIR/fsaverage
@SUMA_Make_Spec_FS -sid fsaverage
suma -spec $SUBJECTS_DIR/fsaverage/SUMA/fsaverage_both.spec
This will give you SUMA displays that look almost identical to the Freesurfer views (like in qdec or Freeview or tksurfer).
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Peter Molfese
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AFNI Message Board
Hi Tracy
You just need to change the resampling method to Nearest Neighbors (default is linear) since it's a segmentation:
adwarp -apar anat+acpc -dpar aseg.nii -prefix aseg_acpc -resam NN
Also, you can view the segmentation in AFNI.
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Peter Molfese
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AFNI Message Board
One thing to consider is that the thickness.niml.dset files that @SUMA_Make_Spec_FS outputs are not smoothed. I believe you could use SurfSmooth to fix this. Alternatively, within the Freesurfer subject's surf directory there are files that are already smoothed and resampled to the fsaverage. To use these within the AFNI toolchain, you can use mris_convert:
mris_convert -c ./Subject0
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Peter Molfese
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AFNI Message Board
While I can make some guesses as to what is going on here, it would be helpful to see your script (or the relevant parts) and the output of 3dinfo -verb YourROIDataset+tlrc. How did you create your ROIs?
That said, it sounds like you are using 3dmaskave, which can work with the "newer" range selectors. If you wish to only extract values for an ROI that has a value of 3, you could
by
Peter Molfese
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AFNI Message Board