AFNI Message Board

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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August 03, 2018 10:13AM
Well, if a program (tedana in this case) is messing up the header info, then, well... the header info might be messed up.

There are two properties here: space and av_space; the latter is the "view" one. For example, the output of this 3dinfo command on the TT_N27 is given here:
3dinfo -prefix -space -av_space /data/REF_TEMPLATES_AFNI/TT_N27+tlrc.
      TT_N27	TLRC	+tlrc

Sounds like you want to change the *space*. I will cite the 3drefit help for both, which are conveniently neighboring:
-view code      Changes the 'view' to be 'code', where the string 'code'
                  is one of 'orig', 'acpc', or 'tlrc'.
               ** WARNING: The program will also change the .HEAD and .BRIK
                  filenames to match.  If the dataset filenames already
                  exist in the '+code' view, then this option will fail.
                  You will have to rename the dataset files before trying
                  to use '-view'.  If you COPY the files and then use
                  '-view', don't forget to use '-newid' as well!
               ** WARNING2: Changing the view without specifying the new 
                  might lead to conflicting information. Consider specifying
                  the space along with -view
  -space spcname  Associates the dataset with a specific template type, e.g.
                  TLRC, MNI, ORIG. The default assumed for +tlrc datasets is
                  'TLRC'. One use for this attribute is to use MNI space
                  coordinates and atlases instead of the default TLRC space.
               ** See WARNING2 for -view option.
... note those WARNING2 comments (which are missing a word, yes: "without specifying the new [space] might lead to conflicting information....", but hopefullyi the meaning is clarified in the next sentence).

See in your 3dinfo output the line:
Template Space:  ORIG
which conflicts with the "view" property. I think your sitation is exactly what is being WARNING2ed against.

Note: I don't think a figure can be "underlayless". It probably just just selecting the offending olay itself, or perhaps some other file in that space (which may not even appear in teh FOV, potentially).

--pt
Subject Author Posted

ETAC, fatal errors - perhaps due to compression?

dowdlelt July 27, 2018 09:20AM

Re: ETAC, fatal errors - perhaps due to compression?

dowdlelt July 30, 2018 04:14PM

Re: ETAC, fatal errors - perhaps due to compression?

dowdlelt August 02, 2018 02:57PM

Re: ETAC, fatal errors - perhaps due to compression?

ptaylor August 02, 2018 07:54PM

Re: ETAC, fatal errors - perhaps due to compression?

dowdlelt August 03, 2018 09:10AM

Re: ETAC, fatal errors - perhaps due to compression?

ptaylor August 03, 2018 10:13AM

Re: ETAC, fatal errors - perhaps due to compression?

dowdlelt August 03, 2018 12:03PM

Re: ETAC, fatal errors - perhaps due to compression?

ptaylor August 03, 2018 01:37PM

Re: ETAC, fatal errors - perhaps due to compression?

dowdlelt August 08, 2018 10:14AM

Re: ETAC, fatal errors - perhaps due to compression?

rick reynolds August 06, 2018 09:37AM

Re: ETAC, fatal errors - perhaps due to compression?

dowdlelt August 08, 2018 10:15AM

Re: ETAC, fatal errors - perhaps due to compression?

rick reynolds August 08, 2018 10:22AM

Re: ETAC, fatal errors - perhaps due to compression?

dowdlelt August 08, 2018 12:04PM