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
