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" greve@nmr.mgh.harvard.edu To: "Kushal Kapse" kkapse@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"greve@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
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