Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

tkregsiter2 problem
by Guang Zeng 20 Aug '09

20 Aug '09

Hi, there, I have the two scans (001.mgz and 002.mgz) of the same subject, 001.mgz is used as the input of recon-all .... -autorecon1, now I have a brainmask.mgz using 001.mgz, I want to register 002.mgz using brainmask.mgz as reference volume, which command I can use? tkregister2? Thanks a lot! Guang _________________________________________________________________ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=PID23391::T:WLMTAGL:ON:WL:en-US:…

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Re: [Freesurfer] mris_fix_topology
by Bruce Fischl 20 Aug '09

20 Aug '09

yes. The only time I've seen this error is when the surface file didn't finish writing. You can load the defects with something like: tksurfer -orig orig.nofix $subject $hemi inflated.nofix then load the curvature file $hemi.defect_labels. You should be able to use save point/goto point in tksurfer and tkmedit to figure out where each vertex is in the wm.mgz volume and manually correct it (although this is an acquired skill!). You may need to specifiy -white orig.nofix as well, although looking at the code I don't think you do. cheers, Bruce On Thu, 20 Aug 2009, Falk Lüsebrink wrote: > Hi Bruce, > > No, there are some hundreds of GB left. > > Is the other topology fixer you meant before mris_topo_fixer? > > Thanks in advance, > Falk > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Thursday, August 20, 2009 4:44 AM > To: Falk Lüsebrink > Cc: freesurfer(a)nmr.mgh.harvard.edu; 'Douglas N Greve' > Subject: Re: [Freesurfer] mris_fix_topology > > are you out of disk space? > On Thu, 20 Aug 2009, Falk Lüsebrink wrote: > >> Hi Doug, >> >> I get the following error: >> >> rh.orig: face[161898].v[2] = 82472, but face 161898 not in vertex >> 82472 face list >> >> Falk >> >> -----Original Message----- >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N >> Greve >> Sent: Thursday, August 20, 2009 12:12 AM >> To: Falk Lüsebrink >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] mris_fix_topology >> >> >> It was not mris_fix_topology that failed but mris_euler_number (but >> that might have failed because of something in the topology fix). What >> happens if you: >> >> cd /home/falk/freesurfer/subjects/yv98_05mm_div >> mris_euler_number ../surf/rh.orig >> >> doug >> >> Falk Lüsebrink wrote: >>> >>> Hi FreeSurfers, >>> >>> >>> >>> Attached is a log file containing an error of mris_fix_topology and I >>> would like to know how to fix that issue if that is possible. Is it >>> possible to view a defect (in that case #33) in tksurfer or freeview >>> to identify a possible error in the wm.mgz or filled.mgz to correct >>> it manually? >>> >>> >>> >>> Thanks in advance, >>> >>> Falk >>> >>> --------------------------------------------------------------------- >>> --- >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > >

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Re: [Freesurfer] thickness map
by Feng-Xian Yan 20 Aug '09

20 Aug '09

Hi, Thank you for your responses before. I have another problem want to solve. I check the number of vertex for all subjects, but I found that the number of vertex for each subjects and each hemispheres is different. Because I want to compare cortical thickness using vertex-by-vertex, I would to obtain the same vertex number. Therefore, have something to do to obtain the same vertex number, i.e. template the cortical thickness at each vertex for each subject on the fsaverage surface, or other methods? How can I do? Would you get me a hand? Thank you in advance! Feng-Xian 2009/8/18 Feng-Xian Yan <mimigirln(a)gmail.com> > > Thank s for your response. > > So, the coordinates are MNI coordinates, not Talairach coordinates. > > > > Thank you in advance. > > > > Feng-Xian > > > > 2009/8/18 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > >> The values in the asc file are in MNI305 space. You can see this in >> tksurfer with View->Configure->Information and select the mni305 button. >> >> Feng-Xian Yan wrote: >> >>> >>> Thank you for your response. >>> >>> So, you mean that I have to do "mris_convert" two times. One for >>> lh.white.tal.asc, another for lh.thickness.asc. And the Tal coordinates in >>> lh.white.tal.asc file corresponds to the cortical thickness value in >>> lh.thickness.asc file. >>> >>> >>> But, the Tal coordinates in lh.white.tal.asc is difference from the >>> result in the tksurfer tool box. That is to say, when I open this subject by >>> tksurfer, I look at the coordinate of the vertex Tal in the tksurfer tool >>> box, and the coordinate is difference from the coordinates that obtain from >>> the command “mris_convert –c lh.thickness lh.white lh.thickness.asc”. >>> >>> >>> What do have some problems? >>> >>> >>> Thank you in advance! >>> >>> >>> Feng-Xian >>> >>> >>> 2009/8/18 Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto: >>> greve(a)nmr.mgh.harvard.edu>> >>> >>> You have convert the thickness file (lh.thickness) to ascii like >>> you did >>> with the surface (with mris_convert). You will then have two >>> files, and >>> the second file will have the thickness values. >>> >>> doug >>> >>> Feng-Xian Yan wrote: >>> > >>> > Hi, >>> > >>> > Sorry, I don't know what you mean. I know each lines is a vertex and >>> > represent a Tal coordinate, but each lines only contain xyz, but not >>> > contain cortical thickness value of these coordinates. That is >>> to say, >>> > the following is >>> > >>> > Tal x Tal y Tal z >>> > >>> > -13.424789 -125.068245 12.671550 0 >>> > >>> > What’s wrong do I think? >>> > >>> > Thank you in advance. >>> > >>> > Feng-Xian >>> > >>> > 2009/8/18 Douglas N Greve <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> > <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> >>> > >>> > Just convert the lh.thickness to ascii as well. Each line of the >>> > xyz coords corresponds to a line in the thickness ascii >>> (each line >>> > is a vertex). >>> > >>> > >>> > doug >>> > >>> > Feng-Xian Yan wrote: >>> > >>> > >>> > Hi, >>> > >>> > I try it again with you recommend me, but the produced asc >>> > file (lh.white.tal.asc) only contain x, y, z >>> coordinates. (The >>> > following shows that.) >>> > >>> > >>> > #!ascii version of lh.white.tal >>> > >>> > 155006 310008 >>> > >>> > -13.424789 -125.068245 12.671550 0 >>> > >>> > -13.939213 -125.063232 12.714314 0 >>> > >>> > -14.861158 -125.268639 12.404987 0 >>> > >>> > >>> > >>> > But, I want to have cortical thickness value with Tal >>> > coordinates. This file doesn’t satisfy our demand. >>> > >>> > >>> > Our demand should contain two points. >>> > >>> > 1) Each vertex across the mantle was represented with an >>> > estimated value of cortical thickness and these estimated >>> > values of cortical thickness should have their coordinates. >>> > >>> > 2) We want to analysis the cortical thickness difference of >>> > three groups, so we want to the cortical thickness value of >>> > each vertex across each subjects should be matched. That >>> is to >>> > say, the cortical thickness should superimposed on a >>> template >>> > surface like fsaverage. >>> > >>> > Therefore, how do we do to obtain the asc file matching our >>> > demands? >>> > >>> > >>> > Thank you in advance. >>> > >>> > >>> > Feng-Xian >>> > >>> > >>> > >>> > >>> > 2009/8/14 Douglas N Greve <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> > <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> > <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> > <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>>> >>> > >>> > >>> > Try these commands: >>> > >>> > mri_surf2surf --s subject --hemi lh --sval-tal-xyz white >>> > --tval-xyz --tval lh.white.tal >>> > mris_convert lh.white.tal lh.white.tal.asc >>> > >>> > doug >>> > >>> > Feng-Xian Yan wrote: >>> > >>> > >>> > Hi, >>> > >>> > I have some problems want to understand. >>> > >>> > (1) I want to analysis the cortical thickness difference of >>> > three groups. But, three groups (one factor/three levels) of >>> > Freesurfer is not satisfied with our demand. Because we want >>> > to get a thickness difference map that satisfied with >>> the many >>> > voxels containing A group > B group > C group and A >>> group < B >>> > group < C group, Freesurfer can’t do that. So, we want >>> to get >>> > this map by myself and use Matlab or other tool to obtain >>> > that. And, now I want to obtain a file that containing >>> the Tal >>> > coordinate and the thickness value of this coordinate >>> for all >>> > subjects. >>> > >>> > Would you tell me how to get the file that containing >>> the Tal >>> > coordinate and the thickness value of this coordinate? >>> > >>> > (2) Before, I want to use the following command to get the >>> > thickness value. >>> > >>> > The command line is "mri_surf2surf --srcsubject noise0.5_0 >>> > --srcsurfval thickness --sfmt surface --trgsubject >>> noise0.5_0 >>> > --trgsurfval noise0.5_0_tal.xfm --tfmt surface --hemi lh >>> > --sval-tal-xyz orig --tval-xyz", and then i type >>> “mris_convert >>> > lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”. >>> > >>> > But, the result file(lh.thickness.asc) does not contain the >>> > thickness value of this coordinate. >>> > >>> > So, I think these commands have some error. >>> > >>> > (3) Use the command “mris_convert –c lh.thickness lh.white >>> > lh.thickness.asc” to obtain the thickness value of the RAS >>> > coordinates. But, I’m confused about that if I change >>> lh.white >>> > to lh.pail or lh.inflated. >>> > What’s difference for the three? >>> > >>> > (4) And, I ask some problem before. >>> > >>> > Everyone said the result file(lh.thickness.asc) is using RAS >>> > coordinates through “mris_convert –c lh.thickness lh.white >>> > lh.thickness.asc”. But, I have confused about this. When I >>> > open this subject by tksurfer, I look at the coordinate >>> of the >>> > vertex RAS in the tksurfer tool box, and the coordinate is >>> > difference from the coordinates that obtain from the command >>> > “mris_convert –c lh.thickness lh.white lh.thickness.asc”. >>> > So, which one is right? >>> > >>> > Thank you in advance! >>> > >>> > Feng-Xian >>> > >>> ------------------------------------------------------------------------ >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@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 >>> <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >>> > <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> >>> > <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> >>> > >>> > Phone Number: 617-724-2358 Fax: 617-726-7422 >>> > >>> > In order to help us help you, please follow the steps in: >>> > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> > >>> > >>> > >>> > -- >>> > Douglas N. Greve, Ph.D. >>> > MGH-NMR Center >>> > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >>> > Phone Number: 617-724-2358 Fax: 617-726-7422 >>> > >>> > In order to help us help you, please follow the steps in: >>> > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> > >>> > >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> In order to help us help you, please follow the steps in: >>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> >

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Error in calabel step.
by Hui Zheng 20 Aug '09

20 Aug '09

Hi freesurfer, We need some technical support here. The dataset was processed successfully using earlier version. But it failed for the lastest 4.50 FS. Here's the message before the process ended. ---------------------------------------------------------------------- Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (768 voxels, overlap=0.418) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (768 voxels, peak = 13), gca=12.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak CSF = 0.21286 (38) gca peak Left_Accumbens_area = 0.43211 (73) gca peak Left_VentralDC = 0.15967 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.64914 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30751 (31) gca peak Right_Accumbens_area = 0.30024 (83) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.81716 (35) gca peak WM_hypointensities = 0.15205 (86) gca peak non_WM_hypointensities = 0.08849 (55) gca peak Optic_Chiasm = 0.34859 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.86 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux neuron 2.6.9-42.ELsmp #1 SMP Tue Aug 15 10:35:26 BST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Aug 20 10:23:28 SGT 2009 ---------------------------------------------------------------------- Any idea why? Thanks in advance. Zheng Hui

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Re: [Freesurfer] mris_fix_topology
by Bruce Fischl 20 Aug '09

20 Aug '09

are you out of disk space? On Thu, 20 Aug 2009, Falk Lüsebrink wrote: > Hi Doug, > > I get the following error: > > rh.orig: face[161898].v[2] = 82472, but face 161898 not in vertex 82472 face > list > > Falk > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, August 20, 2009 12:12 AM > To: Falk Lüsebrink > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_fix_topology > > > It was not mris_fix_topology that failed but mris_euler_number (but that > might have failed because of something in the topology fix). What > happens if you: > > cd /home/falk/freesurfer/subjects/yv98_05mm_div > mris_euler_number ../surf/rh.orig > > doug > > Falk Lüsebrink wrote: >> >> Hi FreeSurfers, >> >> >> >> Attached is a log file containing an error of mris_fix_topology and I >> would like to know how to fix that issue if that is possible. Is it >> possible to view a defect (in that case #33) in tksurfer or freeview >> to identify a possible error in the wm.mgz or filled.mgz to correct it >> manually? >> >> >> >> Thanks in advance, >> >> Falk >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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frontal gray matter and frontal white matter volumes
by Jared Price 20 Aug '09

20 Aug '09

Hi freesurfer gurus, We are doing some freesurfer processing for a collaborating lab and the PI has asked us for a measure of gray matter volume and a measure of white matter volume, both of which need to be specific to just the frontal lobes. Does anyone know of a simple, and accurate, way of acquiring these measures from freesurfer? Thanks. Jared

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Re: [Freesurfer] mris_fix_topology
by Bruce Fischl 19 Aug '09

19 Aug '09

you can view them on the inflated.nofix surface. I think the defect labels are written to curvature format files called ?h.defect_labels or something like that. You might also try using the new topology fixer (Nick can point you at it if you can't find it) cheeers Bruce On Wed, 19 Aug 2009, Falk Lüsebrink wrote: > Hi FreeSurfers, > > > > Attached is a log file containing an error of mris_fix_topology and I would > like to know how to fix that issue if that is possible. Is it possible to > view a defect (in that case #33) in tksurfer or freeview to identify a > possible error in the wm.mgz or filled.mgz to correct it manually? > > > > Thanks in advance, > > Falk > >

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Re: [Freesurfer] mris_fix_topology
by Douglas N Greve 19 Aug '09

19 Aug '09

Hmmm, not sure what's going on, may have to wait for Bruce. Have you looked at the ?h.orig.nofix in tkmedit/tksurfer? Falk Lüsebrink wrote: > Hi Doug, > > I get the following error: > > rh.orig: face[161898].v[2] = 82472, but face 161898 not in vertex 82472 face > list > > Falk > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, August 20, 2009 12:12 AM > To: Falk Lüsebrink > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_fix_topology > > > It was not mris_fix_topology that failed but mris_euler_number (but that > might have failed because of something in the topology fix). What > happens if you: > > cd /home/falk/freesurfer/subjects/yv98_05mm_div > mris_euler_number ../surf/rh.orig > > doug > > Falk Lüsebrink wrote: > >> Hi FreeSurfers, >> >> >> >> Attached is a log file containing an error of mris_fix_topology and I >> would like to know how to fix that issue if that is possible. Is it >> possible to view a defect (in that case #33) in tksurfer or freeview >> to identify a possible error in the wm.mgz or filled.mgz to correct it >> manually? >> >> >> >> Thanks in advance, >> >> Falk >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] mris_fix_topology
by Douglas N Greve 19 Aug '09

19 Aug '09

It was not mris_fix_topology that failed but mris_euler_number (but that might have failed because of something in the topology fix). What happens if you: cd /home/falk/freesurfer/subjects/yv98_05mm_div mris_euler_number ../surf/rh.orig doug Falk Lüsebrink wrote: > > Hi FreeSurfers, > > > > Attached is a log file containing an error of mris_fix_topology and I > would like to know how to fix that issue if that is possible. Is it > possible to view a defect (in that case #33) in tksurfer or freeview > to identify a possible error in the wm.mgz or filled.mgz to correct it > manually? > > > > Thanks in advance, > > Falk > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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mris_fix_topology
by Falk Lüsebrink 19 Aug '09

19 Aug '09

Hi FreeSurfers, Attached is a log file containing an error of mris_fix_topology and I would like to know how to fix that issue if that is possible. Is it possible to view a defect (in that case #33) in tksurfer or freeview to identify a possible error in the wm.mgz or filled.mgz to correct it manually? Thanks in advance, Falk

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