Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug
On 05/25/2012 04:56 PM, Kushal Kapse wrote:
orig.mgz file is on 15446_03908/mri/orig.mgz
yes the subject name and the directory path is correct....
----- 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 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space
The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was
15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls
If either of those are not correct, then it will not determine the path correctly.
Does that orig.mgz file exist?
On 05/25/2012 04:50 PM, Kushal Kapse wrote:
i was talking about this issue....
mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file
i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this
thanks kk
----- Original Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Douglas N Greve"greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space
@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"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@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"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@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"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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer