And it does not intersect the other hemi, I assume? I don't think there's really anthing you can do about it.
doug
Morgan Hough wrote:
Trying again.
-M
Doug Greve wrote:
oops, no image attached!
Morgan Hough wrote:
Hey Doug,
Sorry, what I meant was between the left and right surfaces like in the image that I attached.
Cheers,
-Morgan
Doug Greve wrote:
What do you mean by "between the average surfaces"? Between the white and pial? There are various projection options, eg, you can average between them or take the max. This type of comparison is always a bit ill-posed because the surface in a 3d talairach imbedding space is not that meaningful. You might try mapping your surface-based results into the talairach volume.
doug
Morgan Hough wrote:
Hi Doug,
Multiple versions are always a concern since we have multiple platforms but I have checked them all and I get
$Id: mri_vol2surf.c,v 1.26 2006/02/09 16:31:29 greve Exp $
on all platforms.
I think my problems with the actual output now are due to the problems of trying to project MNI group results onto the average surface - sometimes the results fall between the average surfaces. When viewed in tkmedit you can see why it is not mapping all the MNI group results to the surface. Do you think any projection distance changes would make sense to get a rough approx. of what the t-stats are closest to in this case?
Cheers,
-Morgan
Doug Greve wrote:
Morgan Hough wrote:
> Hi Nick, > > The file looks fine in mri_info and it is convertible to mgz. If > I convert it to Analyze (which I can view using fslview) the > mri_vol2surf command works. Happy to send the files along if > they would be helpful.
Hmmm, that's strange. It's not a float2int issue. It's having problems opening that file. It is strange because it uses exactly the same code that mri_info and mri_convert use to open it. Is is possible that you have mixed versions? Maybe the vol2surf version you have is older?
> > I was trying to get a rough approximation of MNI152 space group > results projected onto the average surface by registering the > volumetric group results with FS's mni305 template and using an > identity reg.dat as the srcreg. I have done this but the results > look wrong. I have checked the registration of the group results > to the mni305 template. Is there anything else I could check? > Should I be doing this differently?
That sounds correct. If the reg looks ok, then you can load your t map onto fsaverage in tkmedit along with the surfaces and see whether they intersect your activation.
doug
> > Cheers, > > -Morgan > > Nick Schmansky wrote: > >> Morgan, >> >> I'm not so sure this is a float2int problem (but Doug may be >> able to >> answer when he gets back next week). Can you read that .nii.gz >> file >> with mri_info? Can you convert it to, say, an .mgz file using >> mri_convert? The error message looks like it can't interpret >> the file >> as a NIFTI file (the preceeding float2int message being >> misleading in >> this instance, I think). >> >> Nick >> >> >> On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote: >> >> >>> Hi there, >>> >>> I am trying to interpolate a volume of tstats to the average >>> surface with mri_vol2surf but I am getting the error below. >>> Does mri_vol2surf take all the inputs that mri_convert takes? >>> Is this a float2int problem mentioned in the bugs section of >>> the --help? If the latter, what argument should I specify with >>> --float2int? Thanks in advance for your time. >>> >>> Cheers, >>> >>> -Morgan >>> >>> mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject >>> average --hemi lh --surf inflated --surfreg lh.sphere.reg >>> --out lh.vbm_surf_results.mgh --srcreg reg.dat >>> srcvol = vbm_results_mni305_tl.nii.gz >>> srcreg = reg.dat >>> srcregold = 0 >>> srcwarp unspecified >>> surf = inflated >>> hemi = lh >>> trgsubject = average >>> surfreg = lh.sphere.reg >>> interp = nearest >>> float2int = round >>> INFO: float2int code = 2 >>> niiRead(): error opening file >>> /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz >>> >>> ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24 >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> >> >> >> > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >