Dear Doug,

thanks for the  immediate response. Actually I checked  the registration with 
freeview/tkregister2 and print out the quality values which are perfectly fine 

I did the following fMRI-analysis steps

FSFAST
1. Preproc-sess (for smoothwm as well as fsaverage space)  --> 
register.dof6.dat in bold/001 and bold/002 folders
2. Selxavg-sess on created design matrices and contrasts (one of the 1st-level 
stat files is called EX.sm5.lh)

3. And  interrogated the results with mris_surfcluster (EX.sm5.lh/EX/ includes 
the sig.nii ces.nii as well as txt.files with the mris_surfcluster output)


The main problem is the creation of .mgh files as inputs used for ROI-analysis 
in the mri_segstats cmd. So the conversion of the sig.nii ces.nii into sig.mgh 
and ces.mgh (using mri_vol2vol)
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview

How to transfer the surface nii.gz files into .mgh files used in volume space?

Thanks,

Christopher



-----Ursprüngliche Nachricht-----
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve
Gesendet: Donnerstag, 2. Juli 2015 14:49
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion

How did you create the EX.sm5.lh analysis? It is probably the case that it is 
already on the surface in which case you don't need to run vol2surf.
doug

On 07/02/2015 04:54 AM, Milde, Christopher wrote:
> Dear Freesurfers,
>
> I have problems converting .nii.gz files into .mgh files needed e.g. 
> for performing ROI analysis.
>
> I used mri_vol2surf and mri_vol2vol to produce .mgh files either to 
> visualize contrast estimates and significance maps on volumes or 
> surfaces
>
> I think the problem is due to voxel resolution mismatches between 
> source and registration files but I don't know how to solve this problem.
>
> I worked with different registration files: the register.dof6.dat 
> (originally outpu from the preproc-sess) as well as register.dat and 
> register.lta by running bbregister for the template.nii.gz
>
>
> ----------------------------------------------------------------------
> -----------------------------------------------------
> here is an example command:
>
> # resample to surface
>
> mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg 
> $sub/bold/register.lta --projfrac 0.5 \  --interp nearest --hemi lh 
> --o $sub/bold/lh.sig.mgh
>
>
> mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg 
> $sub/bold/register.lta --projfrac 0.5 \
> >  --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh
> srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz
> srcreg = PM_04001/bold/register.lta
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> regio_read_register: loading lta
> reading extra input line subject PM_04001 reading extra input line 
> fscale 0.150000
> WARNING: the voxel resolution in the source volume (1,1,1) differs
>          from that listed in the registration file 
> (2.29167,2.29167,2.99) Reading surface 
> /home/christopher/subjects/PM_04001/surf/lh.white
> Done reading source surface
> Reading thickness 
> /home/christopher/subjects/PM_04001/surf/lh.thickness
> Done
> Mapping Source Volume onto Source Subject Surface
>  1 0.5 0.5 0.5
> using old
> Done mapping volume to surface
> Number of source voxels hit = 5
> Writing to PM_04001/bold/lh.sig.mgh
> Dim: 126553 1 1
>
> ----------------------------------------------------------------------
> ------------------------------------------------------
>
> Thanks,
>
> Christopher
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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