Hmmm, I don't know why it is doing that. Does it really print "using old" after the seg fault was that accidentally pasted in? It should not be printing that twice, maybe it's a clue. doug
On 04/02/2012 10:26 AM, Kaveh Kohan wrote: > I have tried and it did not work (the same seg fault, see below). It > seems that it successfully performs the mapping but it fails in final > step probably saving the results. Is the data format that I used OK? > > I am using Ubuntu 10.10, the version of "mri_vol2surf" is "stable5". > Please let me knoe if more information is required. Thanks. > > ~$ mri_vol2surf --mov fMRI.nii.gz --reg bbregister/fmri-TO-orig.dat > --hemi lh --o ./timeCourse.mgz > srcvol = fMRI.nii.gz > srcreg = bbregister/fmri-TO-orig.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Reading surface > /home/kayhan/test/myproject/control001/tp1/FREESURFER/surf/lh.white > Done reading source surface > Mapping Source Volume onto Source Subject Surface > 1 0 0 0 > using old > Done mapping volume to surface > *Segmentation fault* > using old > > >> On Sun, Apr 1, 2012 at 2:34 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> >> wrote: >> >> Hi Kaveh >> >> use bbregister to register your functional data to the >> surface, then mri_vol2surf to sample it from the volume onto >> the surface and you should be all set. >> >> cheers >> Bruce >> >> On Sun, 1 Apr 2012, Kaveh Kohan wrote: >> >> Hi FreeSurfer Users, >> >> >> I am new to the Freesurfer, I have a question regarding >> mapping of the >> resting state fMRI time courses on the cortex area. I >> apologise in case my >> question is naive. please bear with me: >> >> Is it possible to have time-courses sampled from cortex? >> I mean how can I >> get corresponding time-course for each vertex on the >> cortex ? I know that >> FreeSurfer can produce mask for cortex are but I would >> like to have >> time-courses on the flattened (2D) map; ie assuming that >> cortex is >> flattened, each pixel of the 2D flattened image which >> resides in the cortex >> (I guess it corresponds to a vertex on the cortex >> manifold?) is time-series. >> >> I have ran recon-all on the T1. All of those operation >> were done using a >> third party packages that uses freesurfer namely CMTK >> (http://cmtk.org). I >> do not exactly know how to use "bbregister" to register >> the parcellation on >> the resting-state fMRI image? >> >> I would be thankful if you can help. >> >> >> Thanks >> >> >> >> >> >> >> >> 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 >> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > -- 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
