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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, I have recompiled AFNI and reinstalled SUMA on MAC OS. Everything is fine.
But when I try to get SUMA to talk to AFNI ("t"), I receive an Error:
"SUMA_niml_call: Contacting ...
SUMA_niml_call: Trying shared memory...
++ NI_stream_reopen: Waiting for socket connection......... *Failed*
Warning SUMA_niml_call: Shared memory communcation failed.
.....Error SUMA_niml_call:
by
xiangyang
-
AFNI Message Board
I have get the MTG Roi from an anatomical brain using the script below. This MTG cortical region running from the parietal lobe to the entire length of the temporal lobe through the middle temporal gyrus. But i need to get Angular gyrus from this cortical. How?
#############################
foreach type("MTG 605")
set ROI=(`echo $type | awk '{print $1}'`)
set n
by
xiangyang
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AFNI Message Board
I want to map the" ts_normalized" surf_file to the AFNI volume domain(group level), however, the brick datasets in the generated "lh/rh_ts_normalized_sb_tlrc" file don't have same number of volumes with the original "ts_normalized_tlrc" file.
Why?
foreach infile(ts_normalized)
foreach hemi (lh rh)
3dSurf2Vol \
-spec $spath/group/freesurfer/SUMA
by
xiangyang
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AFNI Message Board
Yes, I'm sure it is right.
And, when i use the same script to map GLM_glt surf_file to the AFNI volume domain(group level), it works!
Why?
foreach hemi (lh rh)
1dcat "$hemi"_"$fn".1D\[0] "$hemi"_"$fn".1D\[6..$n] > "$hemi"_"$fn".dset
3dSurf2Vol \
-spec $spath/group/freesurfer/SUMA/subAvg_"$hemi"+tlrc.sp
by
xiangyang
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AFNI Message Board
I want to map data from a surface domain(te_normalized at individual level) to an AFNI volume domain(group level),but it doesn't work. The script is as follows:
cd $spath/sub01/surface_files
foreach hemi (lh rh)
3dSurf2Vol \
-spec $spath/group/freesurfer/SUMA/subAvg_"$hemi"+tlrc.spec \
-surf_A smoothwm \
-surf_B pial \
-sv $spath/group/subAvg_SurfVol_a
by
xiangyang
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AFNI Message Board
foreach infile(GLM.cbucket)
@auto_tlrc -rmode NN -dxyz 2 \
-suffix _at \
-apar Anatomical_reg_AlndExp_ns_at+tlrc \
-input "$infile"+orig
When the input file is ""$infile"+orig" file, the output is named "$infile"_at+TLRC, by default.
However, when the input file is ""$infile".nii.gz"file, the output is named &qu
by
xiangyang
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AFNI Message Board
I have turn on the SUMA menu -> View -> "Cross Hair" (and similarly for "Node in focus" and "Selected Faceset"),but
still cannot see the crosshair, node highlighter and mesh-triangle highlighter on the SUMA map.
by
xiangyang
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AFNI Message Board
I want to creat a ROI based on a cluster in an activation map
To get the mask, I tried to use the following command:
3dmerge -prefix mask_rs-rw -1clip 2.807 -dxyz=1 -1clust_order 1 173 $spath/glts/GLM_glts_rs-rw+tlrc.'[1]'
######The inputfile "GLM_glts_rs-rw+tlrc.'[1]'" comes from the result of t-test analysis.
But, when i get the mask_rs-rw file, there are
by
xiangyang
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AFNI Message Board
when i open the afni and SUMA graphical interface of the fMRI result, then talk them to make they change together.
After talking, i can just see the active regions in the SUMA graphical interface. However, there is no cross symbol to locate the brain area coordinates on the SUMA. How can i do it? Is there some environment variables of .sumarc need to set?
by
xiangyang
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AFNI Message Board
Thanks for your help. I have found the file.
Thank you again.
xiangyang
by
xiangyang
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AFNI Message Board
I have set an AFNI environment variable in your ~/.afnirc file, but I cannot find how to set the environment variable of suma. Is there a .sumarc file exist? where can I find it?
by
xiangyang
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AFNI Message Board