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 > >> > >> > >> > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
