can you tell us what you mean when you say "the output doesn't work", and how you checked the output on the surface? If you specify mgz as the output format make sure the --out file name ends in .mgz
cheers Bruce On Tue, 29 May 2012, Kushal Kapse wrote: > hi doug, > > as per our last conversation of 4d time series on surface, i did mri_vol2surf > as per tutorial on wiki..i used the new mri_vol2surf which u send me....this > was my command: > > mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi lh --out > spm001-lh.w --out_type paint > > > but i cant find output anywhere....ALSO, i tried having output in mgh and mgz > format...but the output doesnt work... > > i opened tkesurfer and tried to check the output...it doesnt show any > activation on surface......can you plz give ur thought on this > > > thanks > kk > > > ----- Original Message ----- > From: "Douglas 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 8:23:47 PM > Subject: Re: [Freesurfer] fMRI time series in surface space > > I don't think it ever supported w files ... you can use mgh /mgz format. > It will also produce nifti files, but they might not always be legal > nifti files. FreeSurfer will always be able to work with them, but other > software packages might not. > doug > > On 5/25/12 8:19 PM, Kushal Kapse wrote: >> doug, >> >> did try new version..it worked fine...but seems tht new version doesnt >> support .w as output format; like in the tutorial online.....what output >> format does the new version vol2surf likes? >> >> 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 5:59:59 PM >> Subject: Re: [Freesurfer] fMRI time series in surface space >> >> Not that I can think of. Did you try that new version? >> >> On 05/25/2012 05:58 PM, Kushal Kapse wrote: >>> yes ..the registration is nicely aligned and i did check the green-lines >>> alignment in tkregister2 >>> >>> is their any other reason for it showing 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 5:52:41 PM >>> Subject: Re: [Freesurfer] fMRI time series in surface space >>> >>> it works for 4D, we do it all the time. Is the registration good? Did >>> you check it visually with tkregister2? You can visualize it with >>> >>> tkregister2 --mov func.nii.gz --reg register.dat --surfs >>> >>> doug >>> >>> On 05/25/2012 05:45 PM, Kushal Kapse wrote: >>>> well... >>>> >>>> it seems the seg fault occured due to i was using a 4D func file and not >>>> 3d....does the vol2surf does only on 3d func data ?....how would i do that >>>> for 4D time series? >>>> >>>> >>>> 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 5:09:31 PM >>>> Subject: Re: [Freesurfer] fMRI time series in surface space >>>> >>>> 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"<gr...@nmr.mgh.harvard.edu> >>>>> To: "Kushal Kapse"<kka...@mail.med.upenn.edu> >>>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>>> Sent: Friday, May 25, 2012 4:52:37 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"<kka...@mail.med.upenn.edu> >>>>>> To: "Douglas N Greve"<gr...@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"<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 >>>>>>>>>> >>>>>>>>>> > > > 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. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
