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@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@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@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@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
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