Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

Re: [Freesurfer] Problem filling labels
by xmeadow＠uchicago.edu 11 Jul '05

11 Jul '05

Hi, I just opened up freesurfer and did some stuff and I got the following in the logs: surfer: using interface /opt/freesurfer_alpha/lib/tcl/tksurfer.new.tcl The /opt/freesurfer_alpha is correct, but I'm not sure what the tksurfer.new.tcl is. Inside freesurfer_alpha/lib I've got a tcl and tcl.new directory. Iniside those folders I've got: tcl.new/tksurfer.new.tcl tcl.new/tksurfer.tcl tcl/tksurfer.new.tcl.020617 tcl/tksurfer.tcl.020318 tcl/tksurfer.tcl tcl/tksurfer.tcl.040219 tcl/tksurfer.new.tcl tcl/tksurfer.tcl.020107 tcl/tksurfer.tcl.120400 But I don't know which of these I should be using. Is there a way I can check which of these is the correct one? Also, in which preference file to I tell Freesurfer to look at the correct tksurfer.tcl file? Thanks very much. >Xander ---- Original message ---- >Date: Fri, 8 Jul 2005 17:35:18 -0400 (EDT) >From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Problem filling labels >To: Xander Meadow <xmeadow(a)uchicago.edu> > > >Actually, I just veried that those are the correct versions to be used >together. > >The only other thing I can think of is that the binary is finding a >different version of the script. When you run tksurfer, look for a line of >output that looks like: > >surfer: using interface .../tksurfer.tcl > >and make sure the .../ part is $FREESURFER_HOME/lib/tcl. Then make sure >that 'which tksurfer' is pointing to the same $FREESURFER_HOME >installation. > > >On Fri, 8 Jul 2005, Xander Meadow wrote: > >> I'm not entirely sure where we got our current version from. If the easiest >> thing to do would be just e-mail me the new script then I am definitely in >> favor of that. I have other machines with freesurfer on them, and it's >> likely they all have this problem, would the easiest thing to do, be to just >> download a new fresh copy of freesurfer from the freesurfer website? But, >> please if it's not too much trouble, send me the new script so I can install >> that and start drawing. Thank you again so much for helping me with this. >> >> >>> Xander >> >> On Jul 8, 2005, at 3:39 PM, Kevin Teich wrote: >> >>> >>> Yes, that version is from 2004, while the script file you're using is from >>> 2003. Did you get a new version from us at some point? If so, you should've >>> gotten a corresponding tksurfer.tcl file. If not, I can give you one. >>> >>> On Fri, 8 Jul 2005, Xander Meadow wrote: >>> >>>>> freesurfer_alpha/bin/tksurfer --all-info >>>> ProgramName: tksurfer ProgramArguments: --all-info ProgramVersion: $Name: >>>> $ TimeStamp: 05/07/08-20:36:58-GMT CVS: $Id: tksurfer.c,v 1.61 2004/01/05 >>>> 20:36:23 fischl Exp $ User: xmeadow Machine: andrew Platform: Linux >>>> PlatformVersion: 2.6.9-11.ELsmp CompilerName: GCC CompilerVersion: 29600 >>>> >>>>> Xander >>>> >>>> On Jul 8, 2005, at 3:26 PM, Kevin Teich wrote: >>>> >>>>> Ah, I think the version of tksurfer you are using is much newer than the >>>>> one that should be associated with the script. What do you get if you >>>>> try: >>>>> tksurfer --all-info >>>>> On Sat, 9 Jul 2005 xmeadow(a)uchicago.edu wrote: >>>>>> Hi, >>>>>> It used to work in the past, but I don't know what might have >>>>>> changed. The machines run uptodate each night to stay current >>>>>> with Redhat patches, but I'm not sure what might have been >>>>>> updated right before this stopped working. As for tksurfer >>>>>> --version >>>>>> freesurfer_alpha/bin/Linux/tksurfer --version >>>>>> $ >>>>>> I'm not sure what the means though, as it's not a number, just >>>>>> the dollar sign. Does this give you any clues? Thanks so >>>>>> much for helping me out with this. >>>>>>> Xander >>>>>> ---- Original message ---- >>>>>>> Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) >>>>>>> From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >>>>>>> Subject: Re: [Freesurfer] Problem filling labels >>>>>>> To: xmeadow(a)uchicago.edu >>>>>>> I can't duplicate this at all. Has this ever worked for you, >>>>>> or did it >>>>>>> stop working? >>>>>>> Can you give me the output of >>>>>>> tksurfer --version >>>>>>> On Fri, 8 Jul 2005 xmeadow(a)uchicago.edu wrote: >>>>>>>> In the Fill box the one I am trying to use is "Up to and >>>>>>>> including boundaries" by itself, but I've also tried the other >>>>>>>> possible combinations in a hope that it would work. Also, >>>>>>>> this error always happens regardless of whatever else I've >>>>>> done. >>>>>>>>> Xander >>>>>>>> ---- Original message ---- >>>>>>>>> Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) >>>>>>>>> From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >>>>>>>>> Subject: Re: [Freesurfer] Problem filling labels >>>>>>>>> To: Xander Meadow <xmeadow(a)uchicago.edu> >>>>>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> What were your settings in the Fill dialog box? Does this >>>>>>>> always happen, >>>>>>>>> or only with a specific combination of options? >>>>>>>>> On Thu, 7 Jul 2005, Xander Meadow wrote: >>>>>>>>>> Hi, >>>>>>>>>> I was trying to make an ROI on an inflated surface. >>>>>>>> Specifically I can >>>>>>>>>> recreate the error if I: >>>>>>>>>> Mark a bunch of vertices >>>>>>>>>> Create fill boundary >>>>>>>>>> clear all marked vertices >>>>>>>>>> mark a vertex within the filled boundary >>>>>>>>>> then try to fill it. >>>>>>>>>> I did all this via the GUI. >>>>>>>>>> Does this help? Is there anything else I can tell you that >>>>>>>> might help? >>>>>>>>>>> Xander >>>>>>>>>> On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: >>>>>>>>>>>> Here is the file you requested: >>>>>>>>>>> Hm, that appears to be OK. What action were you performing >>>>>>>> when you got the >>>>>>>>>>> error? >>>>>>>>>>>> Can you send me the file: >>>>>>>>>>>> $FREESURFER_HOME/lib/tcl/tksurfer.tcl >>>>>>>>>>>> On Thu, 7 Jul 2005 xmeadow(a)uchicago.edu wrote: >>>>>>>>>>>>> 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. >>>>>>>>>>> -- >>>>>>>>>>> Kevin Teich >>>>>>>>> -- >>>>>>>>> Kevin Teich >>>>>>> -- >>>>>>> Kevin Teich >>>>> -- >>>>> Kevin Teich >>>> >>>> >>>> >>> >>> -- >>> Kevin Teich >>> >> >> >> > >-- >Kevin Teich >

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Original surface and sphere correspondence
by Ngo Trung Thanh 10 Jul '05

10 Jul '05

Hi, After mapping the brain surface onto a sphere, we have the surface files. Is there anyway that we can know the correspondence (or the transformation) between the points on the original surface and those on the sphere? Thanks a lot. Best, ntt __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Web tool for visualizing Talairach and MNI locations in 3D volume and on the cortical surface
by David L. Woods 08 Jul '05

08 Jul '05

Freesurfer users who are interested in viewing the location of MNI and Talairach coordinates on the cortical surface or in 3D may be interested in visiting the "Martinez Flat-Mapper" site at http://www.ebire.org/hcnlab/cortical-mapping. Entering MNI or Talairach coordinates will display them on the cortical surface in relation to average gyral anatomy and in a representative 3D brain (Colin). The cortical surface maps are averages of the left and right hemispheres of 40 subjects as viewed with equal area projections that can be centered on temporal, occipital, or frontal lobes. Three different map types are available: cortical curvature, thickness, and fiber directionality (derived from the anisotropic water diffusion). There is also a high-resolution map of average auditory cortex curvature extracted using local landmark techniques. Clicking on a location on any map will display the MNI and Talairach coordinates of the point and show its location in 3D space in the Colin brain. Conversely, clicking on any location in the Colin brain will display that point on the cortical surface maps and provide an estimate of its distance to the gray/white boundary. David L. Woods, Professor of Neurology, Dept. of Neurology,UC Davis, Chief, Clinical Neurophysiology and Chief, Research fMRI imaging, Neurology Service (127E), Building R4, VANCHCS, 150 Muir Rd., Martinez, CA 94553 Tel (925) 372-2571, Fax (925) 229-2315 Email:dlwoods@ucdavis.edu Website: http://marva4.ebire.org/hcnlab

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Re: [Freesurfer] Problem filling labels
by xmeadow＠uchicago.edu 08 Jul '05

08 Jul '05

Hi, It used to work in the past, but I don't know what might have changed. The machines run uptodate each night to stay current with Redhat patches, but I'm not sure what might have been updated right before this stopped working. As for tksurfer --version freesurfer_alpha/bin/Linux/tksurfer --version $ I'm not sure what the means though, as it's not a number, just the dollar sign. Does this give you any clues? Thanks so much for helping me out with this. >Xander ---- Original message ---- >Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) >From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Problem filling labels >To: xmeadow(a)uchicago.edu > > >I can't duplicate this at all. Has this ever worked for you, or did it >stop working? > >Can you give me the output of > >tksurfer --version > >On Fri, 8 Jul 2005 xmeadow(a)uchicago.edu wrote: > >> In the Fill box the one I am trying to use is "Up to and >> including boundaries" by itself, but I've also tried the other >> possible combinations in a hope that it would work. Also, >> this error always happens regardless of whatever else I've done. >> >>> Xander >> >> ---- Original message ---- >>> Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) >>> From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Problem filling labels >>> To: Xander Meadow <xmeadow(a)uchicago.edu> >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> >>> What were your settings in the Fill dialog box? Does this >> always happen, >>> or only with a specific combination of options? >>> >>> >>> On Thu, 7 Jul 2005, Xander Meadow wrote: >>> >>>> Hi, >>>> >>>> I was trying to make an ROI on an inflated surface. >> Specifically I can >>>> recreate the error if I: >>>> >>>> Mark a bunch of vertices >>>> Create fill boundary >>>> clear all marked vertices >>>> mark a vertex within the filled boundary >>>> then try to fill it. >>>> >>>> I did all this via the GUI. >>>> >>>> Does this help? Is there anything else I can tell you that >> might help? >>>> >>>>> Xander >>>> >>>> On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: >>>> >>>>>> Here is the file you requested: >>>>> >>>>> Hm, that appears to be OK. What action were you performing >> when you got the >>>>> error? >>>>> >>>>> >>>>> >>>>>> Can you send me the file: >>>>>> >>>>>> $FREESURFER_HOME/lib/tcl/tksurfer.tcl >>>>>> >>>>>> >>>>>> On Thu, 7 Jul 2005 xmeadow(a)uchicago.edu wrote: >>>>>> >>>>>>> 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. >>>>>> >>>>> -- >>>>> Kevin Teich >>>>> >>>> >>>> >>>> >>> >>> -- >>> Kevin Teich >>> >> >> >> > >-- >Kevin Teich >

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Re: [Freesurfer] Problem filling labels
by xmeadow＠uchicago.edu 08 Jul '05

08 Jul '05

In the Fill box the one I am trying to use is "Up to and including boundaries" by itself, but I've also tried the other possible combinations in a hope that it would work. Also, this error always happens regardless of whatever else I've done. >Xander ---- Original message ---- >Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) >From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Problem filling labels >To: Xander Meadow <xmeadow(a)uchicago.edu> >Cc: freesurfer(a)nmr.mgh.harvard.edu > >What were your settings in the Fill dialog box? Does this always happen, >or only with a specific combination of options? > > >On Thu, 7 Jul 2005, Xander Meadow wrote: > >> Hi, >> >> I was trying to make an ROI on an inflated surface. Specifically I can >> recreate the error if I: >> >> Mark a bunch of vertices >> Create fill boundary >> clear all marked vertices >> mark a vertex within the filled boundary >> then try to fill it. >> >> I did all this via the GUI. >> >> Does this help? Is there anything else I can tell you that might help? >> >>> Xander >> >> On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: >> >>>> Here is the file you requested: >>> >>> Hm, that appears to be OK. What action were you performing when you got the >>> error? >>> >>> >>> >>>> Can you send me the file: >>>> >>>> $FREESURFER_HOME/lib/tcl/tksurfer.tcl >>>> >>>> >>>> On Thu, 7 Jul 2005 xmeadow(a)uchicago.edu wrote: >>>> >>>> > 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. >>>> >>> -- >>> Kevin Teich >>> >> >> >> > >-- >Kevin Teich >

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Re: [Freesurfer] Problem filling labels
by Xander Meadow 07 Jul '05

07 Jul '05

Hi, I was trying to make an ROI on an inflated surface. Specifically I can recreate the error if I: Mark a bunch of vertices Create fill boundary clear all marked vertices mark a vertex within the filled boundary then try to fill it. I did all this via the GUI. Does this help? Is there anything else I can tell you that might help? >Xander On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: >> Here is the file you requested: > > Hm, that appears to be OK. What action were you performing when you > got the error? > > > >> Can you send me the file: >> >> $FREESURFER_HOME/lib/tcl/tksurfer.tcl >> >> >> On Thu, 7 Jul 2005 xmeadow(a)uchicago.edu wrote: >> >> > 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. >> > -- > Kevin Teich >

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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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