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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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Hi,
Yes, the TEST worked. Here are the three steps:
A) afni –ver output:
(base) Mac-Pro-de-Neurociencia:SUMA neurociencia$ afni -ver
Precompiled binary macos_10.12_local: Oct 2 2020 (Version AFNI_20.3.00 'Vespasian')
B) Surf Smooth response:
(base) Mac-Pro-de-Neurociencia:SUMA neurociencia$ SurfSmooth -spec std.141.FT_lh.spec -surf_A std.141.lh.smoothwm.gii -met HEAT_07 -
by
franciscoara
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AFNI Message Board
Ok,
I´ll run this with data camp and explore the afni_proc.py option. std141 has been giving me problems, with some subjects the SurfSmooth tells me there is no such a file in the directory, but there they are.
Thank you very much for your suggestions.
by
franciscoara
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AFNI Message Board
Hi, Some months ago I asked for your help on this error
(base) Mac-Pro-de-Neurociencia:Semantic_Priming neurociencia$ tcsh Script3A
++ 3dTstat: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ 3dcalc: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
++ Authored by: A cast of thousands
++ 3dTstat: AFNI version=AFNI_20.3.00 (Oct 2 2020) [64-bit]
by
franciscoara
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AFNI Message Board
Hi again,
I have run the @SUMA_Make_Spec_FS using -GNIFTI flag. It gave me the meshes std.141 as gii, and used them in my script of SurfSmooth instead of the std.141.lh.smoothwm.asc as shown:
foreach conds ("Nopal" "Norel" "Rel" "Xnopal" "Xnorel" "Xrel")
foreach h (lh rh)
SurfSmooth -spec $SUMA_path/std.141.${subj}_"$h
by
franciscoara
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AFNI Message Board
Hi again,
I have run the @SUMA_Make_Spec_FS using -GNIFTI flag. It gave me the meshes std.141 as gii, and used them in my script of SurfSmooth instead of the std.141.lh.smoothwm.asc as shown:
foreach conds ("Nopal" "Norel" "Rel" "Xnopal" "Xnorel" "Xrel")
foreach h (lh rh)
SurfSmooth -spec $SUMA_path/std.141.${subj}_
by
franciscoara
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AFNI Message Board
Hi,
Thank you for your response. We were not using -GNIFTI options due to the note of problems in SUMA_Make_Spec:
** Note: from 22 Feb 2013 through 20 Mar 2017, use of -NIFTI
would distort standard mesh surfaces. To evaluate
effects of this, consider: MapIcosahedron -write_dist.
And that is why we were using MapIcosahedron to build a mesh in this sc
by
franciscoara
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AFNI Message Board
Hi Taylor,
Thank you very much for your help. This is what I ran in the script with these subjects and previous data.
## After FS recon-all:
@SUMA_Make_Spec_FS -sid ${subj} -debug 1
## Create meshes
foreach h (lh rh)
MapIcosahedron -spec ${subj}_"$h".spec -ld 140 -prefix mesh140. -NN_dset_map $h.aparc.a2009s.annot.1D.roi -all_surfs_spec -verb
by
franciscoara
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AFNI Message Board
Hi,
Thank you for your answer, yes I have another data from other experiments before and it ran well with those (the only difference is, apart from the task and subjetcs, that these data is from a 1.5 T machine, using a TR=3.5s, while the other is from a 3 T machine, using TR=1.5 s). Yes, I have the paths like this in the script:
set top_path = /Users/neurociencia/Desktop/Semantic_Priming/
by
franciscoara
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AFNI Message Board
Hi,
I´ve been trying to run a smooth on a subject surface with this command in a script:
SurfSmooth -spec $SUMA_path/mesh140.${subj}_"$h".spec \
-surf_A mesh140."$h".smoothwm.asc \
-met HEAT_07 -input $data_path/"$h"_${subj}_decon_$condition.TENT.ave_.niml.dset \
-target_fwhm 6 -Niter -1 \
-output $data_path/"$h"_${subj}_decon_$
by
franciscoara
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AFNI Message Board