@doug no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated
----- 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 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: > doug, > > thanks doug....before i do that....i have two questions which may take care > of "mri_vol2surf" issues > > > 1- mri_vol2surf command needs to specify register.dat file........ > > i have been using register.dat file for vol2surf from reg-feat2anat > output.....is that the register.dat file i am supposed to used?.....or if i > am wrong, which register.dat file am i suppose to use....basically, where > does tht file come from No, you are correct > > 2- vol2surf needs functional file as src and register.dat file....are these > both supposed to be in same directory....because during processing it says > "cannot find target reference for orig.mgz"...... They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug > > > please let me know > > thanks > kk > > ----- 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 4:08:35 PM > Subject: Re: [Freesurfer] fMRI time series in surface space > > 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 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 . 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