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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
The Haskins atlas is smaller in size than the TT_N27 or the MNI, reflecting the size of the brain differences in children compared to either 152 adults or Colin. The issue is really normalizing the pediatric data to the adult template or the adult data to a pediatric template.
You could try to make a nonlinear warp between the two spaces (Colin --> Haskins) and then warp the stat map or c
by
Peter Molfese
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AFNI Message Board
There's really not a perfect solution. We know that aligning pediatric data to adult templates is not ideal. The basics are:
1. At age 6, cerebral volume is about 95% of that of an adult (Lenroot & Giedd, 2006).
2. However, grey matter follows an inverted U-shape, which peaks at different times for different cortical (and subcortical) regions (Lenroot & Giedd, 2006).
3. In g
by
Peter Molfese
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AFNI Message Board
It's possible that specifying a -master or -mast_dxyz may help... However - if you're planning to do things in group (standard) space, then I suspect you'd have the best luck downloading the SUMA surfaces for either TT_N27 or MNI and using those segmentations to do your ROI analysis.
There's some problem with using a standard affine warp for moving your segmentations up t
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Peter Molfese
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AFNI Message Board
To correlate the beta maps for each subject with a questionnaire, you can use 3Tcorr1D. Some instructions on that method here.
You can also use 3dMEMA or 3dttest++ with only a single group defined and convert the t-statistic to a correlation. Instructions for that are here.
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Peter Molfese
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AFNI Message Board
This is probably due to changes in X11. If you look at this page and specifically the part about flat_namespace, which depends partially on which shell you're using (bash vs. tcsh):
echo 'export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace' >> ~/.bashrc
If that doesn't work, please provide us the output of:
afni_system_check.py -check_all
by
Peter Molfese
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AFNI Message Board
I suspect the differences would be quite small. Typically EPI images are collected in the axial plane and anatomical (T1) are collected in the sagittal plane. My experience is that in general one does not get noticeable improvement by doing alignment to the in-session anatomical vs. another anatomical of the same subject. There are exceptions to this, but using an average anatomical or templat
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Peter Molfese
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AFNI Message Board
That's certainly an edge case for both #1 and #2.
If it were me, I would create the average template brain (average of the two session high-res images) and align the functional EPI to that. Is there a reason you really want to use the individual session high-res images? I would expect the end result to be similar.
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Peter Molfese
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AFNI Message Board
The first suggestion I would have is to update your binaries. There have been a few tweaks to 3dXClustSim since April 12th.
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Peter Molfese
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AFNI Message Board
Sounds like something may not be quite right in your 3dLME command. Can you please post the full command and output?
Also the info from:
afni_system_check.py -check_all
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Peter Molfese
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AFNI Message Board
I haven't double checked the direction of the warp. If your tests look correct then you could go with that.
Importantly, I think the correct thing (in terms of matrices) is to leave the identity matrix on the first two columns (or just leave them as they are). Placing actual zeros doesn't make much sense. Aligning an object with itself would yield the following matrix:
1 0
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Peter Molfese
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AFNI Message Board
It's been a while since I wrote that post (http://blog.cogneurostats.com/?p=302) on rotating b-vectors. 3dAllineate and 3dWarpDrive both output a base-to-input matrix for the transform. However, while align_epi_anat.py uses 3dAllineate in my command, it will output two matrices, and I choose the one that seemed to make more sense to me - the matrix aligning the DWI to the anatomical datase
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Peter Molfese
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AFNI Message Board
Individuals in my group have found some changes in numpy seem to be causing some issues. Would you mind posting the following outputs?
From terminal:
afni_system_check.py -check_all
From a python shell:
import python
numpy.version.version
import scipy
scipy.__version__
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Peter Molfese
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AFNI Message Board
There's another program called slow_surf_clustsim.py that you can use. However it doesn't yet include the improvements (ACF and permutations) that Bob has been making to 3dFWHMx, 3dClustSim and 3dttest++.
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Peter Molfese
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AFNI Message Board
If AFNI is in your path, it should "just work". The instructions for setting up AFNI in the recommended way are here.
Otherwise you could run it by adding the directory prefix onto the command. But I would really suggest adding AFNI to your path.
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Peter Molfese
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AFNI Message Board
It's based on Freesurfer segmentations, so that's why the names are a bit funny. To get a complete list:
whereami -atlas Haskins_Pediatric_Nonlinear_1.0 -show_atlas_code
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Peter Molfese
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AFNI Message Board
Yes, the rough ACPC or "Axilization" of data... I'm still testing how much impact this has, but the folks at TORTOISE tell me it's a good idea. You can specify a "reorientation" image, which can be your brain.nii file and it'll warp it back to that at the end.
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Peter Molfese
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AFNI Message Board
Hi Jared-
Nice to know someone reads the blog!
I tend to use the -T2pial option with Freesurfer 6, which seems to do a pretty decent job handling dura for me. This has been true whether I'm using a standard T1 MRPAGE or a MEMPRAGE. You could collect just one T1 (MEMPRAGE), but I would stay vigilant about making sure that your T1 is good quality and not contaminated with motion. No
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Peter Molfese
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AFNI Message Board
I've found the differences to be pretty small overall. But the pipeline I currently work with is to take the two anatomical (MPRAGE/MEMPRAGE) scans and put them both into Freesurfer. Depending on your theoretical interests, you could do this in the longitudinal pipeline or as two inputs to the same recon-all (in the more traditional model of dealing with motion). I then run @SUMA_Make_Spe
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Peter Molfese
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AFNI Message Board
What is your actual command? There's actually no command for siemenstoafni in the distribution. You probably want to use Dimon or a program like dcm2nii (part of mricron).
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Peter Molfese
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AFNI Message Board
I don't see a problem with the general methodology of using 3dFWHMx and 3dClustSim (with -acf). The evaluation of the impact of -acf within those tools (3dFWHMx and 3dClustSim) has been focused on the functional data, and while the Eklund paper does say that anatomical data shared similar problems to functional data, I'm not sure if the problem exists to the same extent. For what it
by
Peter Molfese
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AFNI Message Board
Daniel's suggestion is probably easier and likely about the same end result. I might suggest you use Freesurfer to build an unbiased anatomical template using their Longitudinal pipeline. Then using their version of an unbiased brain, I would run @SUMA_Make_Spec_FS to generate a NIFTI version of brain.mgz (now brain.nii) and use that as your skull-stripped anatomical for future processing
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Peter Molfese
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AFNI Message Board
I would do something like this:
3dbucket -aglueto sample.nii subject1.stats_REML+tlrc.HEAD \
subject2.stats_REML+tlrc.HEAD \
... \
subjectX.stats_REML+tlrc.HEAD
Or you could use a for loop in bash (or other scripting language):
for aSubject in subject*.stats_REML+tlrc.HEAD
do
3dbucket -aglueto sample.nii ${aSubject}.stats_REML+tlrc.HEAD
done
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Peter Molfese
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AFNI Message Board
That usually means that a reboot will fix it so XQuartz automatically launches in the future.
by
Peter Molfese
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AFNI Message Board
Can you post the results of running the following command on your system?
afni_system_check.py -check_all
by
Peter Molfese
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AFNI Message Board
You can use 3dTsplit4D (really designed for large files with lots of sub-bricks) or creative use of 3dTcat:
3dTcat -prefix newVol1.nii.gz oldVol+tlrc.HEAD[1]
3dTcat -prefix newVol2.nii.gz oldVol+tlrc.HEAD[2]
by
Peter Molfese
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AFNI Message Board
I think the spaces are throwing off your commands. Try using an underscore:
whereami -mask_atlas_region TT_Daemon:left:nucleus_accumbens -prefix LNAcc
whereami -mask_atlas_region TT_Daemon:left:Brodmann_area_25 -prefix BA25
by
Peter Molfese
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AFNI Message Board
Please post the following so we can check it out.
1. afni_proc.py command
2. path to your data on your local computer
3. the output of afni_system_check.py -check_all
-Peter
by
Peter Molfese
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AFNI Message Board
A Brainhack, part of the Brainhack Global Effort, will take place on the NIH campus in Bethesda, MD on March 2nd and 3rd, 2017. Brainhacks are unique events that convene researchers from across the globe and a myriad of disciplines to work together on innovative projects related to neuroscience. Please join us for this 2-day event and become part of this community of brain enthusiasts working on
by
Peter Molfese
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AFNI Message Board