Ok, I feel I am tantalizingly close... It seems my confusion stemmed from the belief that the mask needed to be in label format, but I've since worked out that it can be loaded in tksurfer in analyze format as an overlay. Now that I can view my mask on the surface, the question is how can I obtain the thickness for the region under the overlay? I thought I could use the -t option in mris_anatomical stats with the mask, but it doesn't seem to read the file and results in 0 thickness (see below). Is a label the only way to obtain thickenss for an ROI? I tried mri_vol2roi and obtained an ROI in bfloat format, but am unsure how to display this in tksurfer, or convert this into a label (it didn't work with the -t command either). The --label argument seems to require a label to already be in place. Thanks for your help! A.
mris_anatomical_stats -t ./186_corconv_native_testmask_binary_y.img 1000186 lh pial using thickness file ./186_corconv_native_testmask_binary_y.img. reading volume /data/flanders/work/alex/freesurfer/subjects/1000186/mri/wm... reading input surface /data/flanders/work/alex/freesurfer/subjects/1000186/surf/lh.pial... MRISreadCurvature: could not open ./186_corconv_native_testmask_binary_y.img No such file or directory Computing inter-vertex distance computing second fundamental form...done. total white matter volume = 659946 mm^3 total surface area = 123477 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm integrated rectified mean curvature = 30613.737 integrated rectified Gaussian curvature = 7478.872 folding index = 3110.626 intrinsic curvature index = 338.606 avg inter-vertex dist (mm) = 1.00548 +/- 0.427572 avg vertex radius (mm) = 61.0534 +/- 17.1529 -----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
