Sorry Doug, Could you please give me an example of how I would implement this? Thanks, Alex
-----Original Message----- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 7/5/2005 1:40 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] mri_vol2surf Something like this should work: vertex_coords = read_surf('lh.white') [w,v] = read_wfile(wfilename); lindex = v; lxyz = vertex_coords(lindex); lvals = zeros(size(lindex)); write_label(lindex, lxyz, lvals, labelfile, subjid); On Mon, 4 Jul 2005, Bruce Fischl wrote: > Hi Alex, > > I think Doug has a .m file to do this in matlab. We'll put an mri_vol2label > on the to-do list, or maybe extend vol2roi to do it. > > Bruce > > On Mon, 4 Jul 2005, Fornito, Alexander wrote: > >> Never mind about the differences between tkmedit and tkregister - I >> retained --regheader in the command line, even though the mask and the >> volume were already correctly aligned, which caused them to move out of >> alignment. However, I'm still unsure of what the correct file format is for >> me to apply the image as an ROI to the surface to get regional anatomical >> info. >> Thanks, >> Alex >> >> -----Original Message----- >> From: Bruce Fischl [mailto:[EMAIL PROTECTED] >> Sent: Mon 7/4/2005 11:25 AM >> To: Fornito, Alexander >> Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] mri_vol2surf >> >> >> >> Hi Alex, >> >> no, label files are text files with the extension .label that >> usually >> reside in the subject's label directory. .w files are "weight" files >> (from EEG/MEG inverse solutions), and more generally, are a sparse >> set of >> floating point values. You can load them in tksurfer with file->load >> overlay, and leave the register field blank. but they probably aren't >> the >> right format for a label, which is just a list of voxels. Maybe Doug >> can >> point you in the right direction for that (mri_vol2roi?) >> >> cheers, >> Bruce >> >> >> On Mon, 4 Jul 2005, Fornito, Alexander wrote: >> >> > Hi, >> > I've managed to get the mask to a point where it's in the correct >> position if I load it through tkmedit (as a binary in analyze format). I >> then run mri_vol2surf, which seems to work (output below). However, If I >> try to load the mask (now saved as a .w file) though tksurfer as file > >> label > load, nothing happens (nothing happens if I try to load it as an >> overlay with the register.dat file either). If I try to load it as a label >> in tkmedit, I get the following: >> > >> > Couldn't load the label. >> > Tkmedit couldn't read the label you specified. This could be >> because the format wasn't valid or the file wasn't found. >> > >> > Am I missing something? I though .w was the correct format for >> labels of this type. >> > Here's the mri_vol2surf output. Thanks again! >> > >> > mri_vol2surf --src 186_corconv_native_testmask_binary_y --src_type >> analyze --srcreg register.dat --hemi lh --out >> ./186_native_flip_y_mask_surf.w --out_type paint >> > INFO: output format is paint >> > srcvol = 186_corconv_native_testmask_binary_y >> > srctype = analyze >> > srcreg = register.dat >> > srcregold = 0 >> > srcwarp unspecified >> > surf = white >> > hemi = lh >> > interp = nearest >> > float2int = round >> > INFO: float2int code = 0 >> > INFO: analyzeRead(): found 1 files for >> /data/flanders/work/alex/freesurfer/subjects/186_corconv_native_testmask_binary_y >> > ----------------------------------------------------------------- >> > INFO: could not find >> /data/flanders/work/alex/freesurfer/subjects/186_corconv_native_testmask_binary_y.mat >> >> file for direction cosine info. >> > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse >> unflipped (default). >> > INFO: if not valid, please provide the information in >> /data/flanders/work/alex/freesurfer/subjects/186_corconv_native_testmask_binary_y.mat >> >> file >> > ----------------------------------------------------------------- >> > INFO: analyzeRead(): min = 0, max = 1 >> > INFO: chaning type to float >> > Done loading volume >> > Reading surface >> /data/flanders/work/alex/freesurfer/subjects/1000186/surf/lh.white >> > Done reading source surface >> > Mapping Source Volume onto Source Subject Surface >> > vol2surf_linear: nhits = 152789/152789 >> > Done mapping volume to surface >> > Number of source voxels hit = 96553 >> > avg = 1.000, stdev = 0.000, min = 1.000, max = 1.000 >> > >> > >> > -----Original Message----- >> > From: Doug Greve [mailto:[EMAIL PROTECTED] >> > Sent: Fri 7/1/2005 10:11 PM >> > To: Fornito, Alexander >> > Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu >> > Subject: Re: [Freesurfer] mri_vol2surf >> > >> > Sorry, I gave you a slightly wrong tkmedit command-line, it should >> have >> > been -overlay-reg ... >> > >> > As for tkmedit, the mask is probably too dark. Click in the window >> and >> > hit 'i'. This will turn on intensity normalization, which will >> probably >> > fix the problem. You may want to load in the volume that you traced >> the >> > mask on instead of the mask itself. >> > >> > doug >> > >> > >> > Fornito, Alexander wrote: >> > >> > >Hi Doug, >> > >I tried the tkmedit command and it loaded the volume with the >> mask, although I got a message saying: >> > >Error: Parsing command line options >> > >Option -reg not recognized >> > >This option was not recognized and ignored. >> > > >> > >Not sure why this occurred, as I loaded it from scratch through >> the GUI (File > Load Overlay Data, with the mask as the volume and >> register.dat as the registration file) and it produced the same with no >> error. >> > >In any case, I can see from tkmedit that the mask is not where it >> should be (It's in the neck, where it should be in the cingulate, above the >> corpus callosum). >> > >However, I tried running tkregister as you suggested to me, and >> although the GUI pops up, I'm unable to see the movable volume (ie., the >> mask). This has happened to me before when i tried something else in >> tkregister, and am not sure if I'm doing anything wrong. The output is >> below. >> > >Thanks for your help, >> > >Alex. >> > > >> > >tkregister2 --s ./1000186 --mov ./186_corconv_mask.img --reg >> ./register.dat --regheader >> > >INFO: no target volume specified, assuming FreeSurfer orig volume. >> > >target volume orig >> > >movable volume ./186_corconv_mask.img >> > >reg file ./register.dat >> > >LoadVol 1 >> > >$Id: tkregister2.c,v 1.22 2003/11/05 21:30:50 greve Exp $ >> > >Diagnostic Level -1 >> > >INFO: analyzeRead(): found 1 files for ./186_corconv_mask.img >> > >----------------------------------------------------------------- >> > >INFO: could not find ./186_corconv_mask.mat file for direction >> cosine info. >> > >INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse >> unflipped (default). >> > >INFO: if not valid, please provide the information in >> ./186_corconv_mask.mat file >> > >----------------------------------------------------------------- >> > >INFO: loading target >> /data/flanders/work/alex/freesurfer/subjects/./1000186/mri/orig >> > >INFO: changing target type to float >> > >Ttarg: -------------------- >> > >-1.000 0.000 0.000 128.000; >> > > 0.000 0.000 1.000 -128.000; >> > > 0.000 -1.000 0.000 128.000; >> > > 0.000 0.000 0.000 1.000; >> > >INFO: loading movable ./186_corconv_mask.img >> > >INFO: analyzeRead(): found 1 files for ./186_corconv_mask.img >> > >----------------------------------------------------------------- >> > >INFO: could not find ./186_corconv_mask.mat file for direction >> cosine info. >> > >INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse >> unflipped (default). >> > >INFO: if not valid, please provide the information in >> ./186_corconv_mask.mat file >> > >----------------------------------------------------------------- >> > >INFO: analyzeRead(): min = 0, max = 1 >> > >INFO: changing move type to float >> > >Tmov: -------------------- >> > >-1.000 0.000 0.000 128.000; >> > > 0.000 0.000 1.000 -128.000; >> > > 0.000 -1.000 0.000 128.000; >> > > 0.000 0.000 0.000 1.000; >> > >mkheaderreg = 1, float2int = 0 >> > >---- Input registration matrix (computed) -------- >> > > 1.000 0.000 0.000 0.000; >> > > 0.000 0.000 1.000 -0.000; >> > > 0.000 -1.000 0.000 0.000; >> > > 0.000 0.000 0.000 1.000; >> > >--------------------------------------- >> > >subject = ./1000186 >> > >Zoom Factor = 2 >> > >---- Input registration matrix -------- >> > > 1.000 0.000 0.000 0.000; >> > > 0.000 0.000 1.000 -0.000; >> > > 0.000 -1.000 0.000 0.000; >> > > 0.000 0.000 0.000 1.000; >> > >Opening window ./1000186 >> > >Setting scale >> > >tkregister2: interface: >> /usr/local/freesurfer/lib/tcl/tkregister2.tcl >> > >tkregister.tcl: startup done >> > >tkregister.tcl: default macro interface (to change: >> macro,mini,micro) >> > >tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro} >> > > >> > > >> > > >> > >-----Original Message----- >> > >From: Doug Greve [mailto:[EMAIL PROTECTED] >> > >Sent: Fri 7/1/2005 12:47 PM >> > >To: Fornito, Alexander >> > >Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu >> > >Subject: RE: [Freesurfer] mri_vol2surf >> > > >> > > >> > >The first thing that you should do is load your mask as an overlay >> in >> > >tkmedit to make sure that it is actually falling where you think >> it >> > >is: >> > > >> > >tkmedit yoursubject orig -overlay ./mask.img -reg ./register.dat \ >> > > -fthresh 0.5 >> > > >> > >The fthresh is set assuming your mask is 0 or 1. You can even load >> > >the surface to see if it actually inersects. >> > > >> > >If this fails, then you need a new registration file. You can >> > >create this with: >> > > >> > >tkregiser2 --s yoursubject --mov mask.img --reg reg.dat >> --regheader >> > > >> > >tkregiser2 allows you to interactively change the registration. >> Note >> > >that you only use --regheader the first time you run it (ie, >> before >> > >you have a reg.dat). >> > > >> > >doug >> > > >> > > >> > > >> > > >> > >On Fri, 1 Jul 2005, Fornito, Alexander wrote: >> > > >> > > >> > > >> > >>Sorry, I forgot to mention, I have the mask in analyze format (I >> traced it in another program). I ran mri_vol2surf using the register.dat >> file format that Doug provided, and got the output below. Although it >> creates a .w file, nothing happens when I load it in tksurfer, I'm gessing >> because the vertex values are zero (?). Have I done something wrong? >> > >> >> > >> mri_vol2surf --src 186_corconv_mask --src_type analyze --srcreg >> register.dat --hemi lh --out ./186_mask_surf.w --out_type paint >> > >>INFO: output format is paint >> > >>srcvol = 186_corconv_mask >> > >>srctype = analyze >> > >>srcreg = register.dat >> > >>srcregold = 0 >> > >>srcwarp unspecified >> > >>surf = white >> > >>hemi = lh >> > >>interp = nearest >> > >>float2int = round >> > >>INFO: float2int code = 0 >> > >>INFO: analyzeRead(): found 1 files for >> /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask >> > >>----------------------------------------------------------------- >> > >>INFO: could not find >> /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask.mat file for >> direction cosine info. >> > >>INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse >> unflipped (default). >> > >>INFO: if not valid, please provide the information in >> /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask.mat file >> > >>----------------------------------------------------------------- >> > >>INFO: analyzeRead(): min = 0, max = 1 >> > >>INFO: chaning type to float >> > >>Done loading volume >> > >>Reading surface >> /data/flanders/work/alex/freesurfer/subjects/1000186/surf/lh.white >> > >>Done reading source surface >> > >>Mapping Source Volume onto Source Subject Surface >> > >>vol2surf_linear: nhits = 152789/152789 >> > >>Done mapping volume to surface >> > >>Number of source voxels hit = 96553 >> > >>Warning: all vertex values are zero >> > >> >> > >> >> > >> >> > >>-----Original Message----- >> > >>From: Bruce Fischl [mailto:[EMAIL PROTECTED] >> > >>Sent: Fri 7/1/2005 11:06 AM >> > >>To: Fornito, Alexander >> > >>Cc: freesurfer@nmr.mgh.harvard.edu >> > >>Subject: Re: [Freesurfer] mri_vol2surf >> > >>Hi Alex, >> > >> >> > >>I think you can just load the label into tksurfer >> (file->label->load) and >> > >>it will sample it onto the surface, assuming that it was drawn on >> one of >> > >>the volumes that the surface was created from (or a coregistered >> one). >> > >>The 1st time you do this it may take a bit, but if you save it >> again it >> > >>will save the vertex #s. >> > >> >> > >>cheers, >> > >>Bruce >> > >> >> > >> >> > >>On Fri, 1 Jul 2005, Fornito, Alexander wrote: >> > >> >> > >> >> > >> >> > >>>Hi, >> > >>>I'm trying apply ROI masks that I've manually traced in volume >> space to the same image's surface using mri_vol2surf. mri_vol2surf seems to >> requires a register.dat file, and I'm unsure what needs to be registered, >> since the volume that I traced the masks on is exactly the same as the one >> that I began with to create the surface (so presumably they are in the same >> space?) . Any hints would be appreciated. >> > >>>Thanks, >> > >>>Alex >> > >>> >> > >>>_______________________________________________ >> > >>>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 >> > >> >> > >> >> > >> >> > > >> > > >> > > >> > >> > >> > >> >> >> >> >> >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
