partial coverage alignment failure

Dear AFNI experts.

I acquired 7T functional data that only covers hippocampus and I browsed through previous related posts and forums ( Aligning Partial Volume fMRI in AFNI | Crash Log ( Based on previous suggestions, there are mainly two steps: adding zero slice and move the origin of the image. However, despite numerous attempts, I am unable to successfully register, which does not cover the hippocampus. The image before registration is shown below.

Thank you for your any kind advice,

Hi, Congcong-

Okeydoke. What is the output of the following, where DSET_ANAT is your underlay anatomical dataset and DSET_SLAB is your overlay slab that covers the hippocampus:

3dinfo -obliquity -prefix DSET_ANAT DSET_SLAB


Also, could you please run the following command, and post the image or images that are produced:

@djunct_overlap_check                                           \
    -ulay    DSET_ANAT                                          \
    -olay    DSET_SLAB                                          \
    -prefix  img_olap

? This will show the initial overlap of the volumes. (And it appears that the tissue contrast of the datasets is effectively opposite---is that right?)


Dear Paul

The first command is as follows:

However, the second command does not generate an image and an error occurred.

Only generate a text as follows:

I'm sorry I'm not very proficient in this command yet.
Thank you for your kindness.

Hi, Congcong-

OK, those datasets are oblique, so we have to be a bit careful about how we overlay/underlay them, which we can get to here.

OK, re. the missing images: you are missing a couple dependencies that you will probably want to have. What is the output of the following (could you please copy+paste the text from the terminal): -check_all



Dear Paul

Thanks for your reminder, I pasted the output text as follows, I apologize for the delay in replying due to the time difference.
Thanks so much

[zhaojing@no-data test_AFNI2]$ -check_all
-------------------------------- general ---------------------------------
architecture:         64bit ELF
system:               Linux
release:              3.10.0-693.el7.x86_64
version:              #1 SMP Tue Aug 22 21:09:27 UTC 2017
distribution:         CentOS Linux 7.9.2009 Core
number of CPUs:       80
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /opt/fox_cloud/share/app/imaging/afni/afni
afni version         : Precompiled binary linux_centos_7_64: Jan  7 2021 
                     : AFNI_21.0.00 'Titus'
AFNI_version.txt     : AFNI_21.0.00, linux_centos_7_64, Jan 07 2021
which python         : /bin/python
python version       : 2.7.5
which R              : /opt/fox_cloud/share/app/imaging/R3.6/bin/R
R version            : WARNING: ignoring environment value of R_HOME
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/opt/fox_cloud/share/app/imaging/afni/afni)
    R       : 1   (/opt/fox_cloud/share/app/imaging/R3.6/bin/R)
    python  : 1   (/usr/bin/python2.7)
    python2 : 1   (/usr/bin/python2.7)
    python3 : 0 

testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success      : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    3dMVM                : success

checking for R packages...
    rPkgsInstall -pkgs ALL -check : success

R RHOME : WARNING: ignoring environment value of R_HOME

checking for $HOME files...
    .afnirc                   : missing
    .sumarc                   : missing
    .afni/help/all_progs.COMP : missing

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
   module file : /usr/lib64/python2.7/site-packages/PyQt4/__init__.pyc

/usr/lib64/python2.7/site-packages/gtk-2.0/gtk/ RuntimeWarning: PyOS_InputHook is not available for interactive use of PyGTK
++ module loaded: matplotlib.pyplot
   module file : /usr/lib64/python2.7/site-packages/matplotlib/pyplot.pyc

-------------------------------- env vars --------------------------------
PATH = /opt/fox_cloud/share/app/imaging/itksnap-3.6.0/bin:/opt/fox_cloud/share/app/imaging/fsl/bin:/opt/fox_cloud/share/app/imaging/matlab2019/bin:/opt/fox_cloud/share/app/imaging/matlab2019/toolbox/distcomp/bin:/opt/fox_cloud/share/app/imaging/dcm2nii/build/bin:/opt/fox_cloud/share/app/imaging/mricron_lx:/opt/fox_cloud/share/app/imaging/R3.6/bin:/opt/fox_cloud/share/app/imaging/ImageMagick6.4/bin:/opt/fox_cloud/share/app/imaging/caret/bin_linux_intel64:/opt/fox_cloud/share/app/imaging/freesurfer6.0/bin:/opt/fox_cloud/share/app/imaging/freesurfer6.0/fsfast/bin:/opt/fox_cloud/share/app/imaging/freesurfer6.0/tktools:/opt/fox_cloud/share/app/imaging/fsl/bin:/opt/fox_cloud/share/app/imaging/freesurfer6.0/mni/bin:/opt/fox_cloud/share/app/imaging/ants/bin:/opt/fox_cloud/share/app/imaging/afni:/opt/fox_cloud/share/app/imaging/MRIConvert-2.0.7/usr/bin:/opt/fox_cloud/share/app/imaging/go/bin:/opt/fox_cloud/share/app/imaging/pycharm/bin:/opt/fox_cloud/share/app/imaging/Qt5.15/5.15.2/gcc_64/bin:/opt/fox_cloud/share/app/imaging/Qt5.15:/Tools/QtCreator/bin:/opt/fox_cloud/system/evn/jdk1.8/bin:/opt/fox_cloud/system/evn/jdk1.8/jre/bin:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/bin:/opt/fox_cloud/share/app/imaging/fsl/bin:/opt/fox_cloud/share/app/imaging/matlab2019/bin:/opt/fox_cloud/share/app/imaging/matlab2019/toolbox/distcomp/bin:/opt/fox_cloud/share/app/imaging/dcm2nii/build/bin:/opt/fox_cloud/share/app/imaging/mricron_lx:/opt/fox_cloud/share/app/imaging/R3.6/bin:/opt/fox_cloud/share/app/imaging/ImageMagick6.4/bin:/opt/fox_cloud/share/app/imaging/caret/bin_linux_intel64:/opt/fox_cloud/share/app/imaging/freesurfer6.0/bin:/opt/fox_cloud/share/app/imaging/freesurfer6.0/fsfast/bin:/opt/fox_cloud/share/app/imaging/freesurfer6.0/tktools:/opt/fox_cloud/share/app/imaging/freesurfer6.0/mni/bin:/opt/fox_cloud/share/app/imaging/ants/bin:/opt/fox_cloud/share/app/imaging/afni:/opt/fox_cloud/share/app/imaging/MRIConvert-2.0.7/usr/bin:/opt/fox_cloud/share/app/imaging/go/bin:/opt/fox_cloud/share/app/imaging/pycharm/bin:/opt/fox_cloud/share/app/imaging/Qt5.15/5.15.2/gcc_64/bin:/opt/fox_cloud/share/app/imaging/Qt5.15:/Tools/QtCreator/bin:/opt/fox_cloud/system/evn/jdk1.8/bin:/opt/fox_cloud/system/evn/jdk1.8/jre/bin:/bin:/usr/bin:/opt/thinlinc/bin:/usr/local/bin:/usr/bin/X11:/sbin:/usr/sbin:/usr/local/sbin:/home/zhaojing/.local/bin:/home/zhaojing/bin

LD_LIBRARY_PATH = /opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/R3.6/lib64:/opt/fox_cloud/share/app/imaging/R:/opt/fox_cloud/share/app/imaging/ImageMagick6.4/lib:/opt/fox_cloud/share/app/imaging/ants/lib:/opt/fox_cloud/share/app/imaging/MRIConvert-2.0.7/usr/lib:/opt/fox_cloud/share/app/imaging/Qt5.15/5.15.2/gcc_64/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/R3.6/lib64:/opt/fox_cloud/share/app/imaging/R:/opt/fox_cloud/share/app/imaging/ImageMagick6.4/lib:/opt/fox_cloud/share/app/imaging/ants/lib:/opt/fox_cloud/share/app/imaging/MRIConvert-2.0.7/usr/lib:/opt/fox_cloud/share/app/imaging/Qt5.15/5.15.2/gcc_64/lib:/opt/thinlinc/lib64:/opt/thinlinc/lib


------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas    : found TT_N27+tlrc  under /opt/fox_cloud/share/app/imaging/afni

------------------------------ OS specific -------------------------------
which yum            : /bin/yum
yum version          : 3.4.3

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  please run: cp /opt/fox_cloud/share/app/imaging/afni/AFNI.afnirc ~/.afnirc
*  please run: "suma -update_env" for .sumarc
*  please run: apsearch -update_all_afni_help
*  insufficient data for AFNI bootcamp

Hi, Congcong-

No need to apologize for not working 24-7! And thanks for posting that.

I guess from the number of CPUs on that computer, and the path location of your AFNI binaries, that that might be some kind of shared, high-performance computer? If so, a solution might involve asking your IT support there to install a couple more dependencies.

Firstly, you can run the following, that are suggested at the bottom of the system check output in the "please fix" section:

cp /opt/fox_cloud/share/app/imaging/afni/AFNI.afnirc ~/.afnirc
suma -update_env 
apsearch -update_all_afni_help

That will populate your default AFNI environment variables and SUMA environment variables, and then setup your system to autocomplete options when typing AFNI commands in the terminal.

Next, your AFNI version is now over 3 years old---I would strongly advise you to update it (or ask your IT to update it). If they cannot do so, you actually could download a set of precompiled binaries under your own directory, and add that location to your path.

But that will likely still require updating some dependencies. In more modern AFNI versions, we check for more dependencies and report that in the output. The list of dependencies for CentOS is here. Perhaps you could share that with your IT, particularly this section? One that is definitely missing on that system is Xvfv (which is installed by that CentOS package manage as xorg-x11-server-Xvfb, as shown in that list of dependencies).

Would you be able to try that, and then we can work on the data question itself?


Dear Paul
You are right, I will ask our IT to resolve these matters and it may take some time.
I will reply as soon as possible once the issue is resolved.
Thanks so much

Can help with MRi brain images. Far as interperation.?

Dear Paul

I'm sorry for the delay in responding to your message due to some unexpected circumstances. I have asked our IT to update AFNI and some dependencies according to your advice, and run the command you have provided.
Thanks so much