Hello, I think that the problem may lie with MRIread.
I have 1 x 82 Array of phase volumes. I also then have a separate 3 x 82 array of coordinates (that correspond to each of the normalized 0 to 1 phase values above. My question is: if I input the phases in vol, what field do I place the coordinates for the phase values in? Many thanks, Jason. On 05/02/2011 01:03, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: try one '-' in '-overlay', not two On Sat, 5 Feb 2011, Jason Connolly wrote: > Hi Bruce, > > I used mri_vol2surf, but there appears to be no overlay colours ... Here is > the output ... > > Any ideas would be great ... > > tksurfer bert rh inflated --overlay > /Applications/fesurfer/subjects/bert/surf/test_LH.mgh > WARNING: flag --overlay unrecognized > WARNING: flag /Applications/freesurfer/subjects/bert/surf/test_LH.mgh > unrecognized > subject is bert > hemi is rh > surface is inflated > surfer: current subjects dir: /Applications/freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /Applications/freesurfer/subjects/bert/mri > surfer: can't create file surfer.log in cwd > surfer: surfer.log created in /tmp > surfer: session root data dir ($session) reset to: > surfer: /tmp > Reading image info (/Applications/freesurfer/subjects/bert) > Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz > surfer: Reading header info from > /Applications/freesurfer/subjects/bert/mri/orig.mgz > ltMNIreadEx: could not open file > /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm > Permission denied > surfer: Talairach xform file not found (ignored) > surfer: vertices=131547, faces=263090 > surfer: single buffered window > surfer: tkoInitWindow(bert) > surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl > Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl > Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl > Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl > Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > > > On 05/02/2011 00:32, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > > no, you can use it to sample volume data onto the surface using > mri_vol2surf > > On Sat, 5 Feb 2011, Jason > Connolly wrote: > >> Can I display register.dat in tksurfer? >> >> Thanks, -j. >> >> >> On 05/02/2011 00:21, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >> that writes the file named register.dat that has the affine registration >> matrix (and some other things) >> >> On >> Sat, 5 Feb 2011, Jason Connolly wrote: >> >>> Hi Bruce, >>> >>> Here it is: >>> >>> bbregister --s bert --mov >>> /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat >>> --bold --init-header >>> >>> -jason. >>> >>> On 05/02/2011 00:18, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >>> >>> can you send us your command line? >>> On Sat, 5 Feb 2011, Jason Connolly wrote: >>> >>>> Hi Doug, >>>> >>>> I am now at the bbregister stage ... I ran this but it is not clear to me >>>> where the output is? I don't see an output flag ... >>>> >>>> Can you tell me where to look for my output? >>>> >>>> Almost there! >>>> >>>> Many thanks, Jason. >>>> >>>> >>>> On 04/02/2011 23:49, "Jason Connolly" <jason.conno...@newcastle.ac.uk> >>>> wrote: >>>> >>>> Thank you. -jason. >>>> >>>> >>>> On 04/02/2011 23:48, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: >>>> >>>> You can load in the functional with MRIread since you are going to be >>>> replacing all the pixel data anyway with your single time point. Just >>>> use the single argument. The second is if you dont want to read in the >>>> pixel data. >>>> >>>> Jason Connolly wrote: >>>>> Thanks. >>>>> >>>>> So, to clarify, I am trying to just make an overlay. So do I use MRIread >>>>> with a functional .img as input? >>>>> >>>>> Is the second argument in MRIread my scanCoords for my phase-value pixels? >>>>> >>>>> Almost there ... >>>>> >>>>> >>>>> >>>>> >>>>> On 04/02/2011 23:35, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: >>>>> >>>>> It's the vol field. >>>>> doug >>>>> >>>>> Jason Connolly wrote: >>>>> >>>>>> Hi Doug, >>>>>> >>>>>> You state: >>>>>> >>>>>> "then replace the pixel data with your >>>>>> analyzed data" >>>>>> >>>>>> I cannot seem to find the field for the pixel data. Can you tell me >>>>>> where to position these values? >>>>>> >>>>>> Thanks! -jason. >>>>>> >>>>>> >>>>>> On 04/02/2011 18:15, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>> You should save it out as nifti (see MRIwrite.m and MRIread.m). I would >>>>>> suggest using MRIread.m to read in your file in order to create the >>>>>> proper header information, then replace the pixel data with your >>>>>> analyzed data, then use MRIwrite.m to save it out. Then use bbregister >>>>>> to register this volume to the anatomical, then use mri_vol2surf to >>>>>> sample it to the surface (either native anatomical or to some other >>>>>> subject). >>>>>> >>>>>> doug >>>>>> >>>>>> Jason Connolly wrote: >>>>>> >>>>>> >>>>>>> Dear freesurfer experts: >>>>>>> >>>>>>> I have been using matlab to analyze a retinotopic dataset. >>>>>>> >>>>>>> However, the 3D volumes are not in standardized space (and I wish to >>>>>>> display multiple maps from different subjects on one surface). >>>>>>> >>>>>>> Although the initial segmentations were done in freesurfer, my question >>>>>>> is: >>>>>>> >>>>>>> Is it possible to take matlab arrays that contain 3D space anatomical >>>>>>> coordinates and phase information (on a voxel by voxel basis) and >>>>>>> display these on a standardized inflated freesurfer-generated surface? >>>>>>> >>>>>>> If so, is the pipeline documented? >>>>>>> >>>>>>> Many thanks, >>>>>>> >>>>>>> Jason. >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> gr...@nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> >>>>>> >>>>>> >>>>>> 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. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> gr...@nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> gr...@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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
