Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug
On 05/25/2012 04:03 PM, Kushal Kapse wrote: > hi dough, > > following is the terminal output which lead to segmentation fault..... > > i checked the data space and it is not out of size > > > > > mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp > trilinear --hemi lh --o lh.func.nii.gz > srcvol = pitt1_cpw-e_4.05_059.nii.gz > srcreg = register.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > ProjFrac = 0.5 > thickness = thickness > reshape = 0 > interp = trilinear > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white > Done reading source surface > Reading thickness > /data/mgi_structural/penn/controls/11186_03197/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 > Segmentation fault > > > ----- Original Message ----- > From: "Douglas N Greve"<gr...@nmr.mgh.harvard.edu> > To: "Kushal Kapse"<kka...@mail.med.upenn.edu> > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, May 25, 2012 3:53:31 PM > Subject: Re: [Freesurfer] fMRI time series in surface space > > Hi Kushal, please be sure to include the entire terminal output. These > kinds of things are hard to track down from just the error msg. Also, > how many time points are in the func.nii.gz? And are you sure that you > are not running out of space on the disk? > doug > > On 05/25/2012 02:57 PM, Kushal Kapse wrote: >> hi, Doug >> >> as per conversation yday, i did perform mri_vol2surf on a functional volume >> to map it in surface space as follows >> >> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp >> trilinear --hemi lh --o lh.func.mgh >> >> it shows me "Done mapping volume to surface" followed by "Segmentation fault" >> >> >> may i please know why it states segmentation fault as i have no clue of >> which segmentation on vol2surf is faulty??? >> >> >> thanks >> kk >> >> >> ----- Original Message ----- >> From: "Douglas N Greve"<gr...@nmr.mgh.harvard.edu> >> To: freesurfer@nmr.mgh.harvard.edu >> Sent: Thursday, May 24, 2012 11:19:21 AM >> Subject: Re: [Freesurfer] fMRI time series in surface space >> >> Why not run the full preprocessing? It will do the sampling (and surface >> smoothing) for you. Alternatively, you can just use mri_vol2surf, then >> mris_fwhm to do the surface smoothing (you can also surface smooth in >> mri_vol2surf so you can do it all with one command). >> doug >> >> On 05/24/2012 08:35 AM, Kushal Kapse wrote: >>>> Hi Everyone, >>>> >>>> I am new to FreeSurfer, and having some issues with what I believe should >>>> be a pretty basic operation. >>>> >>>> My goal is to register a 4D functional time series to FS average space for >>>> further connectivity analysis in Matlab (similar to the recent Yeo et al. >>>> J Neurophysiology paper). We have run recon-all without problems on the >>>> structural data, but I am having trouble getting the whole functional time >>>> series into surface space. When I perform FS-FAST just from pre >>>> processing till automatic registration of func-struc, "register.dof6.dat" >>>> is produced, which includes input registration matrix. Is their any way to >>>> apply this registration matrix to the 4D time series directly, so that the >>>> output is in FS average template surface (rather than volumetric) space? >>>> >>>> Many thanks, >>>> kk >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
