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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March 08, 2019 02:01PM
Thanks for this information. I went ahead and did that but I am still having difficulty getting the group analysis to recognize the GIFTI files - any thoughts?

1. Run conversion from .mgz to .gii
mris_convert -f taskBOLD_nBack_scan_8_lh.mgz $FREESURFER_HOME/subjects/fsaverage/surf/lh.white S1.l.func.gii

2. Use HCP pipeline to align to a standard mesh and merge hemispherse --> dscalar.nii file

3. Run 3dMVM which errors out:
*+ WARNING: NO spatial transform (neither qform nor sform), in NIfTI file 'SST_BOLD_S10_LR.dscalar.nii'
Then it says,

** Error:
Problem with input files! Two possibilities: 1) There is a specification error
with either file path or file name. Use shell command 'ls' on the last column in the
data table to find out the problem. 2) At least one of the input files has different
dimensions. Run "3dinfo -header_line -prefix -same_grid -n4 *.HEAD" in the directory
where the files are stored, and pinpoint out which file(s) is the trouble maker.
Replace *.HEAD with *.nii or something similar for other file formats.

4. 3dinfo -header specified no errors in dimensions between files

3dinfo -header_line -prefix -same_grid -n4 *.func.gii
prefix =grid? Ni Nj Nk Nv
S1.l.func.gii 1 10242 1 1 37
S2.l.func.gii 1 10242 1 1 31


5. Just using the .func.gii files and ignoring the steps to combine the hemispheres and align to a standard mesh, still produces an error stating that the file inputs are problematic.
Subject Author Posted

Freesurfer .mgz to .niml for 3dMVM, 3dLME etc

shanaadise March 05, 2019 02:22PM

Re: Freesurfer .mgz to .niml for 3dMVM, 3dLME etc

ptaylor March 05, 2019 05:59PM

Re: Freesurfer .mgz to .niml for 3dMVM, 3dLME etc

shanaadise March 05, 2019 06:39PM

Re: Freesurfer .mgz to .niml for 3dMVM, 3dLME etc

Peter Molfese March 05, 2019 08:52PM

Re: Freesurfer .mgz to .niml for 3dMVM, 3dLME etc

shanaadise March 08, 2019 02:01PM

Re: Freesurfer .mgz to .niml for 3dMVM, 3dLME etc

Peter Molfese March 08, 2019 02:32PM