Sorry, can you backup and tell me what you are trying to accomplish? doug On 07/02/2015 10:05 AM, Milde, Christopher wrote: > 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 > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at http://www.partners.org/complianceline . If the e-mail was sent to you in > error but does not contain patient information, please contact the sender and > properly dispose of the e-mail. > > > _______________________________________________ > 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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
