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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
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The Research Computing Center at Boston University is looking to hire someone with fMRI experience for a position to support the somewhat new Cognitive Neuroimaging Center. The candidate would provide consulting and scientific application support, including the development, porting, and optimizing of software for computational neuroscience and neuroimaging.
Salary grade 50: Min salary: $76,
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activatedvoxel
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AFNI Message Board
So it was all me. I ran it originally from inside of the surf directory. Everything else ran fine except the extra atlas, so I didn't realize it. Worked once I went inside the main recon-all directory or used the fspath.
Thanks for helping me discover my own stupidity! I have been away from data analysis too long!
Thanks,
Stephanie
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activatedvoxel
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AFNI Message Board
I uploaded the orig dicoms to the box drive you sent. I also included a text file of the files in the FreeSurfer directory. Let me know if that wasn't what you were asking for.
Thanks!
Stephanie
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activatedvoxel
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AFNI Message Board
Thanks for the reply. Let me give some more details about my specific setup then.
Freesurfer version from build-stamp.txt
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Ran it with:
@SUMA_Make_Spec_FS -NIFTI -extra_annot_labels aparc.DKTatlas -sid sub-CSA006 -debug 2
I noticed these lines this time, that also mention the extra label...
++ have 1 extra labels, includin
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activatedvoxel
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AFNI Message Board
Hello,
I am trying to add an additional annotation (DKTatlas). I see there is a new flag, -extra_annot_labels that I think should do what I want.
For reference, I am running:
Precompiled binary linux_openmp_64: Jan 18 2021 (Version AFNI_21.0.04 'Titus')
I used the command:
@SUMA_Make_Spec_FS -NIFTI -extra_annot_labels DKTatlas -sid sub-CSA006
I also tried
@SUMA_Make_Spec
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activatedvoxel
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AFNI Message Board
Just wanted to bump this up, as it is hanging me up and blowing my mind :).
by
activatedvoxel
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AFNI Message Board
Thanks so much for the clarification. I had one follow-up about some weirdness I am seeing within the global output.
I tried it first with two hpowers based on something I had seen in an example:
-ETAC 8 -ETAC_blur 0 2 -ETAC_opt NN=1:sid=2:hpow=0,2:pthr=0.05,0.01:name=Fred1
This resulted in a fair amount of activity surviving the mask.
But then I saw the comments in the etac help which s
by
activatedvoxel
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AFNI Message Board
Hi,
I am running ETAC for the first time and am having trouble figuring out what all the output files are, even after reading the help and a slide deck I found.
I ran ETAC with the following commands:
-ETAC 8 \
-ETAC_blur 0 2 \
-ETAC_opt NN=1:sid=2:hpow=1:pthr=0.05,0.01:name=Fred1 \
-ETAC_opt NN=2:sid=2:hpow=1:pthr=0.05,0.01:name=Fred2 \
I got the following output files:
globalETAC.
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activatedvoxel
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AFNI Message Board
I am wondering what the information from 3dinfo -VERB that gives you the R-to-L center, A-to-P center and I-to-S center are relative to.
We are wondering if we can use this as a measure of how subject's were from each other in the bore of the scanner. Like are they relative to the center of the bore? So it would represent the location of your FOV relative to something concrete? They se
by
activatedvoxel
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AFNI Message Board