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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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Daniel,
Thanks so much for clarifying the function's behavior. I think I have a workaround based on your advice. Appreciate your help!
Best,
Jennifer
by
jbarredo
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AFNI Message Board
Cheers AFNI users!
I am trying to produce a map of voxels ranked by percentile of local intensity using 3dLocalstat. While the distribution of 'hot spots' in the output stats map look correct, the output voxel values are not in terms of percentile (e.g. voxel corresponding to 50th percentile is not 0.5). Am I forgetting to set an additional modifying flag? Any help is appreciated!
by
jbarredo
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AFNI Message Board
Hi Rick,
Thank you, that totally worked! Now however, I'm getting an error stating that there are multiple spec at input. I've gone back to the help, but I haven't found anything that helps with this error. The slow_surf_clustsim.py script didn't have any hints either. I've checked out the .spec and surf_A files and everything looks kosher.
Thanks,
Jennifer
by
jbarredo
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AFNI Message Board
Ooops! I fixed the -spec and the -surf_A flags and confirmed that the files are referenced with the correct path. It's still giving me the option 2 error. Here's what I've entered now:
SurfClust -spec ../../mySpec_lh.spec \
-surf_A ./../lh.pial.asc
-input 'lh.myData.niml.dset[11]' \ ***these are my tstats***
-rmm 2 \
-thresh_col 11 \
-
by
jbarredo
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AFNI Message Board
Hi,
I'm trying to make ROIs on surface data using SurfClust. I'd like to include only nodes where t >of 3.6. I've used the following code to no avail
SurfClust ../../mySpec_lh.spec \
-input lh.myData.niml.dset[11] \ ***these are my tstats***
-rmm 2 \
-thresh_col 11 \
-athresh 3.6
I keep getting an "Option 2 not understood" error. I've looked over
by
jbarredo
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AFNI Message Board
Hi Rick,
3dcalc worked with the .niml.dset files even if 3dmerge did not. Thanks!
by
jbarredo
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AFNI Message Board
Thanks for looking into this Rick and let me know if you need anything.
Best,
Jennifer
by
jbarredo
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AFNI Message Board
Hi Experts,
I would like to make a thresholded map in surface rather than volume space. I've attempted this like so...
3dmerge -1thresh 0.26 -prefix lh.corrThresh lh.myData.niml.dset
However the output doesn't match the map produced by manually adjusting the threshold with the Surface Controller slider, in fact it looks unaltered. Is 3dmerge compatible with surface data or is t
by
jbarredo
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AFNI Message Board
Hi Rick and Ziad,
@Rick: You're right, the correct number of bricks is in the 3dSurf2Vol output. However, I could never get the surf2Vol output to work with 3ddelay.
@Ziad: I tried using the niml file as suggested and it ran successfully with 3ddelay. However, the output looks unexpected...prior to surface smoothing I ran the delay analysis using spatially unsmoothed data and saw retin
by
jbarredo
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AFNI Message Board
Hello,
I've imported some functional data into surface space so I can spatially smooth on the surface. SurfSmooth worked well and the resulting niml file indicates that the correct number of epi volumes (128) are incorporated into the output. I next used 3dSurf2Vol to convert my data back to volume space before running a time delay analysis. Unfortunately, the following error cropped up:
by
jbarredo
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AFNI Message Board
This ended up being a version compatibility problem, not a registration error.
JB
by
jbarredo
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AFNI Message Board
Hi Ziad,
Sorry for the slow reply, I've been snowed in. The registration is still incorrect after adding the GIFTI flag. I've put the data in a compressed tar file, but it's bigger than the allowed attachment size. How shall I send it to you? Thanks again.
Best,
Jennifer
by
jbarredo
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AFNI Message Board
Hi Ziad,
I used the following command:
@SUMA_Make_Spec_FS -fspath ~/data/jbarredo/RET_103
to generate the SUMA files from my Freesurfer surface. When I checked the images as suggested using
suma -spec RET_103_both.spec -sv RET_103_SurfVol+orig
I saw the distorted image I attached to my first post.
Thanks,
Jennifer
by
jbarredo
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AFNI Message Board
Any one have any suggestions? I'm stuck on this step and could use some ideas.
by
jbarredo
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AFNI Message Board
Hi,
The SurfVol files generated by the @SUMA_Make_Spec_FS script are way out of register (image attached, crosshairs ~AC) . The Freesurfer surfaces were generated from a T1 image that was deobliqued in AFNI prior to Freesurfer surface estimation. Here's what I've checked so far:
-- FS surfaces are of good quality when viewed in Freeview.
-- SurfVol file generated by @SUMA script
by
jbarredo
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AFNI Message Board