Freesurfer July 2005

freesurfer@nmr.mgh.harvard.edu

39 participants
68 discussions

Problem filling labels
by xmeadow＠uchicago.edu 07 Jul '05

07 Jul '05

Hi, I'm having trouble filling labels using Freesurfer version 0.9(33y). I'm running RedHat Enterprise WS v.4. I looked through the mail archives and found that this problem has happened in the past, the post is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00042.html I get the same error: Error: Wrong # args: fill_flood_from_cursor dont_cross_boundary dont_cross_label dont_cross_cmid dont_cross_fthresh use_multiple_seeds action argument I have a .xdebug_tkmedit if it would help debug this issue. Does anyone know what I can do to fix this? Thank you very much. >Xander

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Re: [Freesurfer] General Question
by Arvind Gururajan 07 Jul '05

07 Jul '05

Hi, Please do give me some more details. Thanks, Arvind Gururajan On 6 Jul 2005, Bruce Fischl wrote: > yes. Matti can give you details if you're interested. > > On Wed, 6 Jul 2005, Arvind Gururajan wrote: > > > > > Hello all, > > > > I just had a general question about freesurfer. Does freesurfer use > > Boundary element model for realistic human head (not sphere etc) ? > > > > Thanks, > > > > Arvind Gururajan > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >

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General Question
by Arvind Gururajan 06 Jul '05

06 Jul '05

Hello all, I just had a general question about freesurfer. Does freesurfer use Boundary element model for realistic human head (not sphere etc) ? Thanks, Arvind Gururajan

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RE: [Freesurfer] mri_vol2surf
by Fornito, Alexander 06 Jul '05

06 Jul '05

Hi Bruce, I tried to do this this, but custom fill doesn't seem to find the boundaries of the ROI, so it ends up filling everything. I've tried playing with some of the options but it doesn't change anything. Is there a particular set of options that I need to check? Thanks, Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 7/6/2005 11:22 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] mri_vol2surf Hi Alex, you can click inside the ROI region on the surface, then use custom fill to create a label and save it to a file. cheers, Bruce On Wed, 6 Jul 2005, Fornito, Alexander wrote: > 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:greve@nmr.mgh.harvard.edu] > Sent: Tue 7/5/2005 1:40 AM > To: Bruce Fischl > Cc: Fornito, Alexander; freesurfer(a)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:fischl@nmr.mgh.harvard.edu] >>> Sent: Mon 7/4/2005 11:25 AM >>> To: Fornito, Alexander >>> Cc: Doug Greve; freesurfer(a)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:greve@nmr.mgh.harvard.edu] >>> > Sent: Fri 7/1/2005 10:11 PM >>> > To: Fornito, Alexander >>> > Cc: Bruce Fischl; freesurfer(a)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:greve@nmr.mgh.harvard.edu] >>> >>Sent: Fri 7/1/2005 12:47 PM >>> >>To: Fornito, Alexander >>> >>Cc: Bruce Fischl; freesurfer(a)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:fischl@nmr.mgh.harvard.edu] >>> >>>Sent: Fri 7/1/2005 11:06 AM >>> >>>To: Fornito, Alexander >>> >>>Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu >>> >>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>>> >>> >>>> >>> >>>> >>> >>> >>> >>> >>> >>>_______________________________________________ >>> >>>Freesurfer mailing list >>> >>>Freesurfer(a)nmr.mgh.harvard.edu >>> >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>> >>> >>> >> >>> >> >>> >> >>> > >>> > >>> > >>> >>> >>> >>> >>> >>> >> >> >> > >

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RE: [Freesurfer] mri_vol2surf
by Fornito, Alexander 06 Jul '05

06 Jul '05

Success!! (I think) I converted the binary mask to a greyscale image, and it seems like custom fill is able to detect the appropriate boundaries. I created a label from this and was able to generate anatomical stats for the ROI (hooray!). 2 more questions: 1 - when I go back into to tkmedit and load the label of the volume, it appears as a thin line running across the grey-white surface, rather than extending to the pial surface. I'm presuming this is because the label is now in 2D. Is this correct? 2 - Do "total surface area" and "total gray matter volume" only correspond to the label (not the entire surface?), and if so, why do I get a different value for total gray matter volume if I specify pial as the surface than if I specify white as the surface? Thanks again, Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 7/6/2005 11:22 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] mri_vol2surf Hi Alex, you can click inside the ROI region on the surface, then use custom fill to create a label and save it to a file. cheers, Bruce On Wed, 6 Jul 2005, Fornito, Alexander wrote: > 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:greve@nmr.mgh.harvard.edu] > Sent: Tue 7/5/2005 1:40 AM > To: Bruce Fischl > Cc: Fornito, Alexander; freesurfer(a)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:fischl@nmr.mgh.harvard.edu] >>> Sent: Mon 7/4/2005 11:25 AM >>> To: Fornito, Alexander >>> Cc: Doug Greve; freesurfer(a)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:greve@nmr.mgh.harvard.edu] >>> > Sent: Fri 7/1/2005 10:11 PM >>> > To: Fornito, Alexander >>> > Cc: Bruce Fischl; freesurfer(a)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:greve@nmr.mgh.harvard.edu] >>> >>Sent: Fri 7/1/2005 12:47 PM >>> >>To: Fornito, Alexander >>> >>Cc: Bruce Fischl; freesurfer(a)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:fischl@nmr.mgh.harvard.edu] >>> >>>Sent: Fri 7/1/2005 11:06 AM >>> >>>To: Fornito, Alexander >>> >>>Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu >>> >>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>>> >>> >>>> >>> >>>> >>> >>> >>> >>> >>> >>>_______________________________________________ >>> >>>Freesurfer mailing list >>> >>>Freesurfer(a)nmr.mgh.harvard.edu >>> >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>> >>> >>> >> >>> >> >>> >> >>> > >>> > >>> > >>> >>> >>> >>> >>> >>> >> >> >> > >

1 0

RE: [Freesurfer] mri_vol2surf
by Fornito, Alexander 05 Jul '05

05 Jul '05

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:greve@nmr.mgh.harvard.edu] Sent: Tue 7/5/2005 1:40 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer(a)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:fischl@nmr.mgh.harvard.edu] >> Sent: Mon 7/4/2005 11:25 AM >> To: Fornito, Alexander >> Cc: Doug Greve; freesurfer(a)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:greve@nmr.mgh.harvard.edu] >> > Sent: Fri 7/1/2005 10:11 PM >> > To: Fornito, Alexander >> > Cc: Bruce Fischl; freesurfer(a)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:greve@nmr.mgh.harvard.edu] >> > >Sent: Fri 7/1/2005 12:47 PM >> > >To: Fornito, Alexander >> > >Cc: Bruce Fischl; freesurfer(a)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:fischl@nmr.mgh.harvard.edu] >> > >>Sent: Fri 7/1/2005 11:06 AM >> > >>To: Fornito, Alexander >> > >>Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu >> > >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >>> >> > >>> >> > >>> >> > >> >> > >> >> > >>_______________________________________________ >> > >>Freesurfer mailing list >> > >>Freesurfer(a)nmr.mgh.harvard.edu >> > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> >> > >> >> > >> >> > > >> > > >> > > >> > >> > >> > >> >> >> >> >> >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

2 1

avg152T1
by Peter Soros 05 Jul '05

05 Jul '05

Hi All, I have tried to reconstruct the surface of the avg152T1 standard template. The strip skull procedure did not work at all. I tried the procedures explained in the freesurfer manual (p. 30), changing the preflooding height and running without watershed analyze. Unfortunately, that didn't change the result. Are there other solutions how to improve skull stripping? If you need to see the images I obtained, I'd be happy to send them. Your help is very much appreciated! Peter

3 2

RE: [Freesurfer] mri_vol2surf
by Fornito, Alexander 04 Jul '05

04 Jul '05

Sorry Doug, Could you please give me an example of how I would implement this? Thanks, Alex -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 7/5/2005 1:40 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer(a)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:fischl@nmr.mgh.harvard.edu] >> Sent: Mon 7/4/2005 11:25 AM >> To: Fornito, Alexander >> Cc: Doug Greve; freesurfer(a)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:greve@nmr.mgh.harvard.edu] >> > Sent: Fri 7/1/2005 10:11 PM >> > To: Fornito, Alexander >> > Cc: Bruce Fischl; freesurfer(a)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:greve@nmr.mgh.harvard.edu] >> > >Sent: Fri 7/1/2005 12:47 PM >> > >To: Fornito, Alexander >> > >Cc: Bruce Fischl; freesurfer(a)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:fischl@nmr.mgh.harvard.edu] >> > >>Sent: Fri 7/1/2005 11:06 AM >> > >>To: Fornito, Alexander >> > >>Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu >> > >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >>> >> > >>> >> > >>> >> > >> >> > >> >> > >>_______________________________________________ >> > >>Freesurfer mailing list >> > >>Freesurfer(a)nmr.mgh.harvard.edu >> > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> >> > >> >> > >> >> > > >> > > >> > > >> > >> > >> > >> >> >> >> >> >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

1 0

RE: [Freesurfer] mri_vol2surf
by Fornito, Alexander 04 Jul '05

04 Jul '05

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:fischl@nmr.mgh.harvard.edu] Sent: Mon 7/4/2005 11:25 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer(a)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:greve@nmr.mgh.harvard.edu] > Sent: Fri 7/1/2005 10:11 PM > To: Fornito, Alexander > Cc: Bruce Fischl; freesurfer(a)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:greve@nmr.mgh.harvard.edu] > >Sent: Fri 7/1/2005 12:47 PM > >To: Fornito, Alexander > >Cc: Bruce Fischl; freesurfer(a)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:fischl@nmr.mgh.harvard.edu] > >>Sent: Fri 7/1/2005 11:06 AM > >>To: Fornito, Alexander > >>Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu > >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >> > >> > >>_______________________________________________ > >>Freesurfer mailing list > >>Freesurfer(a)nmr.mgh.harvard.edu > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > > > > > > > >

3 2

RE: [Freesurfer] mri_vol2surf
by Fornito, Alexander 03 Jul '05

03 Jul '05

Aahh... that would explain it. I assumed that because you saved labels from the parcellation to get ROI thickness stats, label was the correct format for a manually delineated ROI. I'm probably wrong, but from understanding of the mri_vol2roi --help, it allows me to create a binary ROI from the volume, which is what I already have (albeit mine is in analyze format). What I'm trying to do is apply this ROI to the surface as a mask to get regionally specific anatomical stats (ie., thickness, curvature, etc. info for the manually delineated ROI only). Should I try to obtain the mri_vol2surf output in some other format that would allow me to do this? I'm not sure which would do the trick... Also, another source of confusion is that when I overlay the mask in tkmedit, I get a good fit, but it's in the wrong position when I load it in tkregister2. Why does this happen? Thanks again, A. -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 7/4/2005 11:25 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer(a)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:greve@nmr.mgh.harvard.edu] > Sent: Fri 7/1/2005 10:11 PM > To: Fornito, Alexander > Cc: Bruce Fischl; freesurfer(a)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:greve@nmr.mgh.harvard.edu] > >Sent: Fri 7/1/2005 12:47 PM > >To: Fornito, Alexander > >Cc: Bruce Fischl; freesurfer(a)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:fischl@nmr.mgh.harvard.edu] > >>Sent: Fri 7/1/2005 11:06 AM > >>To: Fornito, Alexander > >>Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu > >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >> > >> > >>_______________________________________________ > >>Freesurfer mailing list > >>Freesurfer(a)nmr.mgh.harvard.edu > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > > > > > > > >

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Freesurfer July 2005