Hi Kushal, you cannot use .w file for 4D outputs. Use this cmd: mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi lh --out spm001.mgh
doug On 5/29/12 8:46 AM, 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
