Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30096 discussions

Editing pial surface
by Lars Tjelta Westlye 12 Sep '05

12 Sep '05

Dear all, I am trying to edit the pial surface by editing/deleting voxels in the brain volume within the pial surface ('labeled' as a part of cortex), but clearly are parts of dura when manually inspected. When I rerun the last automatic procedures (fix, make_final, morph), and check the pial surface, nothing has appeared to have changed. The voxels I deleted are gone, though the pial surface still looks the same. How can I fix this without having to regenerate/reconstruct all my subjects? (I have approx. 100). Any tip? I am by the way using the Freesurfer version from june (?) 2005, and due to time restrictions I am not considering changing to the latest version for this project. Thanks a lot! Best wishes, Lars Tjelta Westlye University of Oslo

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Recon-all in background?
by Brian Schweinsburg, Ph.D. 10 Sep '05

10 Sep '05

Is there a way to run recon-all (the new dev version) in the background, while still saving all the relevant info to the .log and .status files? I tried recon-all -subjid XXX -autorecon-all & but it still sends info to the screen. Thanks, brian

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RE: [Freesurfer] Skull stripping
by Fornito, Alexander 10 Sep '05

10 Sep '05

Does it affect the aseg with respect to the GCA registration? Is so, how perfect does the strip need to be to avoid biasing the aeg results, eg., are small portions of the meninges or skull around the top of the cortex going to affect the results much? I now they can affect the pial surface, but I'd prefer to edit that after the surfaces are created. Thanks again! Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sat 9/10/2005 10:56 AM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull stripping Hi Alex, if the strip removes the cerebellum, then the aseg stuff will fail (if you're using it). If you aren't it doesn't really matter. cheers, Bruce On Sat, 10 Sep 2005, Fornito, Alexander wrote: > Hi all, > Couple of questions re: failures of skull stripping" > - If you edit the brain volume after autorecon1, do you need to re-run autorecon1 again, or van you just continue on to autorecon2? > - Is it a major problem if the strip removes the cerebellum, since it's excluded by the cuttting planes anyway, or does this interfere with finding the cutting planes later on? > Thanks, > Alex > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Skull stripping
by Fornito, Alexander 09 Sep '05

09 Sep '05

Hi all, Couple of questions re: failures of skull stripping" - If you edit the brain volume after autorecon1, do you need to re-run autorecon1 again, or van you just continue on to autorecon2? - Is it a major problem if the strip removes the cerebellum, since it's excluded by the cuttting planes anyway, or does this interfere with finding the cutting planes later on? Thanks, Alex

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resampling talairach
by Tracy Wang 09 Sep '05

09 Sep '05

Hi all, I'm trying to resample an image into a talairach transformed volume from the 256^3 dimensions into 172 x 220 x 156. I've been using mri_convert in the following command line: mri_convert -at transforms/talairach.xfm --devolvexfm 000718_vc4734 -cs 1 -oc -0.0950 -16.51 9.75 -ic 0 0 0 -oic 172 -ojc 220 -okc 156 -odt uchar nu nu_talairach_new3.img It ran very nicely, but the anterior and posterior (frontal and occipital) regions are cut off, like they were cropped off. I suspect it is because data is being conformed to 256^3 in all directions and is just cropping to fit into my specified dimensions, but that is not what i would like to do. How would I be able scale it to fit into my specified dimension? I have tried -sc, but no matter how much smaller i seem to scale it, it's not enough to compensate for the crop. thanks for any help! Tracy Wang Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

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Re: [Freesurfer] mri_normalize
by Sasha Wolosin 09 Sep '05

09 Sep '05

I haven't conformed it, so I'll try that- thanks. -Sasha >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 9/9/2005 3:42 PM >>> Hi Sasha, the problem is that the orig.mgz volume hasn't been "conformed". Did you generate it with recon-all? It should be 1mm isotropic, 256mm^3 and UCHAR instead of SHORT. You could do (from the mri subdir): mv orig.mgz orig_unconformed.mgz mri_convert --conform orig_unconformed orig.mgz then go on your merry way Bruce On Fri, 9 Sep 2005, Sasha Wolosin wrote: > OK, this time it worked: > [wolosin@localhost /freesurfer]# cd $SUBJECTS_DIR/2332/mri > [wolosin@localhost mri]# ls > aseg filled norm segment.dat transforms > brain flash nu.mgz T1 wm > brain.mgz fsamples orig T1.mgz wm-init.mgz > error.log mri rawavg.mgz tmp wm.mgz > [wolosin@localhost mri]# cd orig > [wolosin@localhost orig]# mri_info orig.mgz > Volume information for orig.mgz > type: MGH > dimensions: 256 x 256 x 124 > voxel sizes: 0.9375, 0.9375, 1.5000 > type: SHORT (4) > fov: 240.000 > xstart: -112.5, xend: 112.5 > ystart: -112.5, yend: 112.5 > zstart: -139.5, zend: 139.5 > TR: 35.00 msec, TE: 6.00 msec, TI: 0.00 msec, flip angle: 45.00 degrees > nframes: 1 > ras xform present > xform info: x_r = -0.9981, y_r = -0.0056, z_r = 0.0616, c_r = 0.4646 : x_a = -0.0615, y_a = -0.0131, z_a = -0.9980, c_a = 0.9575 : x_s = 0.0064, y_s = -0.9999, z_s = 0.0127, c_s = 15.7709 > talairach xfm : /home/wolosin/subjects/2332/mri/transforms/talairach.xfm > Orientation LIP > Primary Slice Direction coronal > > voxel to ras transform: > -0.9357 -0.0052 0.0923 115.1803 > -0.0576 -0.0122 -1.4970 102.7195 > 0.0060 -0.9374 0.0190 133.8122 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant 1.31836 > > ras to voxel transform: > -1.0646 -0.0656 0.0068 128.4501 > -0.0060 -0.0139 -1.0666 144.8367 > 0.0410 -0.6653 0.0085 62.4846 > 0.0000 0.0000 0.0000 1.0000 > [wolosin@localhost orig]# > > thanks, > Sasha > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 >>>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 09/09/05 1:48 PM >>> > sorry, you have to run it from the subject's mri dir (or use the full > path) > > On Fri, 9 Sep 2005, Sasha Wolosin wrote: > >> Here is the result: >> >> [wolosin@localhost /freesurfer]# mri_info orig.mgz >> zcat: /freesurfer/orig.mgz.gz: No such file or directory >> mghRead(/freesurfer/orig.mgz, -1): read error >> >> thanks, >> Sasha >> >> Sasha Wolosin >> Research Assistant >> Developmental Cognitive Neurology >> Kennedy Krieger Institute >> 707 N. Broadway >> Baltimore, MD 21205 >> ph: (443) 923-9270 >>>>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 09/09/05 1:23 PM >>> >> Hi Sasha, >> >> can you do: >> >> mri_info orig.mgz >> >> and send us the results? >> >> thanks, >> Bruce >> On Fri, 9 Sep 2005, Sasha Wolosin wrote: >> >>> I am still having problems with mri_normalize. I have downloaded the latest snapshot- but I still get an error: >>> >>> [wolosin@localhost mri]$ mri_normalize orig.mgz T1.mgz >>> reading from orig.mgz... >>> normalizing image... >>> talairach transform >>> 1.103 0.048 -0.007 -4.504; >>> -0.051 1.166 0.004 -13.012; >>> 0.007 -0.003 1.090 -15.454; >>> 0.000 0.000 0.000 1.000; >>> INFO: Modifying talairach volume c_(r,a,s) based on average_305 >>> building Voronoi diagram... >>> performing soap bubble smoothing... >>> 3d normalization pass 1 of 2 >>> white matter peak found at 110 >>> Segmentation fault >>> >>> >>> I thought it might be a problem with the talairach transform, but I can't figure out how to view this properly. >>> >>> [wolosin@localhost subjects]$ tkregister2 --mgz --s 2335 --fstal --surf orig.mgz >>> surfname set to orig.mgz >>> INFO: no target volume specified, assuming FreeSurfer orig volume. >>> target volume orig >>> movable volume (null) >>> reg file (null) >>> LoadVol 1 >>> $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ >>> Diagnostic Level -1 >>> talairach.xfm --------------------- >>> 1.103 0.048 -0.007 -4.504; >>> -0.051 1.166 0.004 -13.012; >>> 0.007 -0.003 1.090 -15.454; >>> 0.000 0.000 0.000 1.000; >>> ERROR: cannot determine type of /home/wolosin/subjects/talairach/mri/orig >>> >>> Do you know what I am missing? >>> Any advice is greatly appreciated, >>> Thanks, >>> Sasha >>> >>> Sasha Wolosin >>> Research Assistant >>> Developmental Cognitive Neurology >>> Kennedy Krieger Institute >>> 707 N. Broadway >>> Baltimore, MD 21205 >>> ph: (443) 923-9270 >>> >>> >>> >>> Disclaimer: >>> The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> > > >

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Fwd: Re: [Freesurfer] mri_normalize
by Sasha Wolosin 09 Sep '05

09 Sep '05

Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270

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mri_normalize
by Sasha Wolosin 09 Sep '05

09 Sep '05

I am still having problems with mri_normalize. I have downloaded the latest snapshot- but I still get an error: [wolosin@localhost mri]$ mri_normalize orig.mgz T1.mgz reading from orig.mgz... normalizing image... talairach transform 1.103 0.048 -0.007 -4.504; -0.051 1.166 0.004 -13.012; 0.007 -0.003 1.090 -15.454; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 white matter peak found at 110 Segmentation fault I thought it might be a problem with the talairach transform, but I can't figure out how to view this properly. [wolosin@localhost subjects]$ tkregister2 --mgz --s 2335 --fstal --surf orig.mgz surfname set to orig.mgz INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.103 0.048 -0.007 -4.504; -0.051 1.166 0.004 -13.012; 0.007 -0.003 1.090 -15.454; 0.000 0.000 0.000 1.000; ERROR: cannot determine type of /home/wolosin/subjects/talairach/mri/orig Do you know what I am missing? Any advice is greatly appreciated, Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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center values
by Tracy Wang 09 Sep '05

09 Sep '05

Hi all, I'm trying to find the anatomical center value of the image volume in the mni average_305 space. Any ideas? -Tracy Wang Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

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Re: [Freesurfer] segmentation fault during make_average_surface Hello Nick, Thanks for your reply, here are the info: mris_make_average_surface -all-info ProgramName: mris_make_average_surface ProgramArguments -all-info ProgramVersion $Name: $ TimeStamp: 05/09/09-07:09:31-GMT CVS: $Id: mris_make_average_surface.c, v 1.9 2004/01/29 14:59:12 tosa Exp $ User: root Machine: ltscopc12 Platform: Linux PlatformVersion: 2.4.21-4 EL CompilerName: GCC CompilerVersion: 29600 cat /etc/redhat-release Red Hat Enterpris
by Marie Schaer 09 Sep '05

09 Sep '05

Hello Nick, Thanks for your reply, here are the info: mris_make_average_surface -all-info ProgramName: mris_make_average_surface ProgramArguments -all-info ProgramVersion $Name: $ TimeStamp: 05/09/09-07:09:31-GMT CVS: $Id: mris_make_average_surface.c,v 1.9 2004/01/29 14:59:12 tosa Exp $ User: root Machine: ltscopc12 Platform: Linux PlatformVersion: 2.4.21-4 EL CompilerName: GCC CompilerVersion: 29600 cat /etc/redhat-release Red Hat Enterprise Linux WS release 3 (Taroon) Thank you very much for your help, Marie On Sep 7, 2005, at 10:55 PM, Nick Schmansky wrote: > Marie, > > It is possible that the version of mris_make_average_surface that you > have is old, and has a bug. Can you tell me the version info? Type: > > mris_make_average_surface -all-info > > And if the -all-info command option is not valid (indicating an old > version), can you type: > > ls -alF mris_make_average_surface > > And what platform are you running on? Type: > > cat /etc/redhat-release > > Nick > > > > On Wed, 2005-09-07 at 11:59 +0200, Marie Schaer wrote: >> >> >> Hello, >> >> I'm trying to make an average surface using the latest version of >> make_average_surface (2005/08/02 19:14:20 nicks Exp), and I got the >> same error >> as posted in the following message: >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ >> msg01135.html, with a >> segmentation fault when mris_average_surface is called (I get the same >> segmentation fault when running mris_average_surface alone): >> >> mris_make_average_surface -i 7 -o orig rh orig_avg sphere.reg >> average_test subj1 >> subj2 >> processing subject subj1... >> The following must be >> revisited******************************************* >> Segmentation fault >> >> >> I did not find in the mailing list how to solve this, thank you very >> much for >> your help, >> >> Marie Schaer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >

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Freesurfer