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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
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Hi AFNI/Suma users,
I'm trying to project several functional data onto the MNI_N27 cortical surfaces and I want to use a same pbar for all dataset so that I'll be able to compare the value differences between those ROIs directly.
I modified several environment variables: AFNI_PBAR_FULLRANGE, AFNI_PBAR_LOCK, AFNI_RANGE_LOCK, AFNI_THRESH_LOCK. I also set AFNI_PBAR_THREE = YES so th
by
Xixi Wang
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AFNI Message Board
Hi Rick,
Thank you for your reply! My original though was like: 1) run recon-all for SPM's MNI152 T1 template in freesurfer and 2) convert the surface to afni format and then use 3dVol2Surf to project my functional data onto cortical surfaces. But I found out that SUMA website has N27 brain surfaces already, so right now what I'm doing is: 1) 3dcopy roi.nii new_afni_file 2) afni -nim
by
Xixi Wang
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AFNI Message Board
Hi all,
I have some functional data for different Harvard-Oxford ROIs and HO ROIs and the functional data have been aligned to SPM's T1 template. I want to display those functional data onto inflated cortical surfaces. My question is 1) shall I perform cortical extraction process based on the T1 template (the resolution is pretty low though) and then use 3dVol2Surf to project the function
by
Xixi Wang
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AFNI Message Board
Hi AFNI/SUMA users,
I overlaid my color-coded surface map onto the inflated hemispheres and displayed them in SUMA. I tried playing with the dimming factor ("dim" button in surface controller) a little bit so that the color and brightness could match with the colorbar I generated in MATLAB best. I was wondering whether I can customize the value via command line instead of surface con
by
Xixi Wang
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AFNI Message Board
Xixi Wang Wrote:
-------------------------------------------------------
> Hi Ziad,
>
> Thank you very much for your reply! The
> mris_convert -c didn't work so I tried:
> mris_convert --annot lh.aparc_parula.a2009s.annot
> lh.inflated lh.aparc_parula.a2009s.annot.gii
> and it worked like a charm!
>
Hi AFNI/SUMA users,
Sorry to bring this up again.
by
Xixi Wang
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AFNI Message Board
Hi Ziad,
Thank you very much for your reply! The mris_convert -c didn't work so I tried:
mris_convert --annot lh.aparc_parula.a2009s.annot lh.inflated lh.aparc_parula.a2009s.annot.gii
and it worked like a charm!
One last question:
I loaded the merged hemispheres ($ suma -spec subj.both.spec) and I tired turning off the bk:Convexity by deselecting the "I" drop box on the
by
Xixi Wang
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AFNI Message Board
Hi AFNI users,
I’ve been stuck with the FSread_annot command and I’m looking forward to get some help from you:
I created cortical surface parcellation with the Destrieux atlas in Freesurfer and then I modified the annotation file (i.e. lh.aparc.a2009s.annot) so that for each ROI, the RGB values correspond to specific decoding accuracy values (namely the brighter the color is, the higher th
by
Xixi Wang
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AFNI Message Board
Hi all,
I’d like to project my activation maps onto cortical surfaces and I got some questions while using different methods.
Method 1: First I initialized both AFNI and SUMA:
afni -niml & suma -spec mh_ico64_al.spec -sv subj_..._SurfVol_ss_al2exp+tlrc
I then let SUMA talk to AFNI. After setting the bold file as underlay (bold.nii) and one activation map as overlay (condition1.nii),
by
Xixi Wang
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AFNI Message Board
Hi Ziad,
Thanks a lot for your reply. It worked!
Best,
Xixi
by
Xixi Wang
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AFNI Message Board
rick reynolds Wrote:
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> Hi XiXi,
>
> You could create some sort of 0,1,2,3
> conjunction map from the 2 results and
> have afni send that to suma.
>
> Or you could run 3dvol2surf on each of
> the datasets you are interested in, and
> then control the mixing of them in suma
> (it is good at that).
&g
by
Xixi Wang
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AFNI Message Board
Hi all,
I'm trying to project and visualize my functional activation maps onto the cortical surface using AFNI and SUMA. The command is like:
$ afni -niml & suma -spec -sv
I then let SUMA talk to AFNI and then selected the bold data (i.e. bold.nii) as underlay and the activation map for VT cortex as overlay (i.e. condition1_VTcortex.nii) so that I could see functional values pro
by
Xixi Wang
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AFNI Message Board