Show all posts by user
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
Page 1 of 1 Pages: 1
Results 1 - 9 of 9
Hi, I was trying my singularity container from afni and everything semed fine unitl i tried de command @SUMA_Make_Spec_FS
It seems like link to /opt/afni/abin/@SUMA_Make_Spec_FS is failing, this is not the case with other @ commands as @Align_Centers. I also downloaded the official AFNI singularity image from the webpage and it seems to have the same problem. Could you help please? thank you in
by
vferrer
-
AFNI Message Board
Hi all,
I was doing a singularity container of AFNI and things seem to be working properly except for the command \@SUMA_Make_Spec_FS, it is giving an error:
\@SUMA_Make_Spec_FS
@global_parse: Command not found.
I actually download the singularity container from AFNI and the same problem keeps happening, could you please help me?
Cheers,
Vicente.
by
vferrer
-
AFNI Message Board
Hy guys,
Do anyone of you know a way of reading afni .1D files in python? Thank you in advance
Cheers,
Vicente
by
vferrer
-
AFNI Message Board
Hi there,
We are trying the new installation of AFNI and SUMA in our cluster and trying my scripts I got the next error:
@SUMA_Make_Spec_FS -NIFTI -fspath $SUBJECTS_DIR/$SUBJ -sid $SUBJ -debug 2
-- usage okay
if ( 0 ) set ldlist = ( )
if ( 0 == 0 && 2 != 0 ) then
set ldpref = (
by
vferrer
-
AFNI Message Board
Hi, I am having problems with 3dskullstrip in ubuntu 18
the command gives this error:
3dSkullStrip: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
it seems that libgsl.so.19 is deprecated because i have installed GNU scientific libraries, you can check that every other library is there:
ldd `which 3dSkullStrip`
linux-vdso.s
by
vferrer
-
AFNI Message Board
Hi I have tried what you say and it doesn't work, after applying @Align_centers the auto_warp.py stops in the affine registration:
@Align_Centers -overwrite -base ${TEMPLATEDIR}/${TEMPLATE} -dset ${SUBJ}_T1_ns_bc.nii.gz -prefix prueba.nii.gz -1Dmat_only
++ 3dcopy: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ 3drefit: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored b
by
vferrer
-
AFNI Message Board
Hi guys,
I am doing a functional to MNI transformation and therefore applying realigment+inv(anat to functional)+anat to MNI in one 3dNwarpApply. My problem is that using the MNI template as master and preserving the voxel size (3mm) the grid of my image is different. Here the 3dNwarpApply command:
3dNwarpApply -master $TEMPLATEDIR/$TEMPLATE -overwrite -dxyz ${VOXELRESZ} \
-so
by
vferrer
-
AFNI Message Board
Hi I have installed afni in ubuntu 18 and the afni_system_check.py -check_all script is giving me some errors:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.15.0-34-generic
version: #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018
distribution: debian buster/sid
by
vferrer
-
AFNI Message Board
Hi there,
In one of my subjects auto_warp.py failed to do the affine step by itself. Therefore I tried to calculate before the affine transform with 3dAllineate:
3dAllineate -base ${TEMPLATEDIR}/${TEMPLATE}'[0]' -input ${SUBJ}_T1_ns_bc.nii.gz -1Dmatrix_save extra.1D -prefix prueba.nii.gz
I checked and the images are aligned successfully. I tried to give the extra.1D matrix to a
by
vferrer
-
AFNI Message Board