it does not produce a .w file the output is spm001.mgh
On 5/29/12 9:00 AM, Kushal Kapse wrote: > hi doug/bruce: > > it still says it cannot find .w file....please check at the bottom .... > > [kkapse@dendrite 15546_03908]$ /home/kkapse/mri_vol2surf.linux --src > func.nii.gz --reg register.dat --hemi rh --out spm001.mgh > srcvol = func.nii.gz > srcreg = register.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = rh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Reading surface /15546_03908/surf/rh.white > Done reading source surface > Mapping Source Volume onto Source Subject Surface > 1 0 0 0 > using old > Done mapping volume to surface > Number of source voxels hit = 10737 > Writing to spm001.mgh > Dim: 147942 1 1 > [kkapse@dendrite 15546_03908]$ qsurfer -stat spm001 -hemi lh -subject > 15546_03908 > ERROR: cannot find 15546_03908/spm001-lh.w > > > 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: Tuesday, May 29, 2012 8:54:40 AM > Subject: Re: [Freesurfer] fMRI time series in surface space > > 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. 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