Freesurfer

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30055 discussions

mri_normalize & mri_fill
by Michele Perry 03 Jun '05

03 Jun '05

I'm still having problems... With control points saved, I did in : mri_normalize -f $SUBJECTS_DIR/<subjid>/tmp/control.dat -no1d $SUBJECTS_DIR/<subjid>/mri/orig $SUBJECTS_DIR/<subjid>/mri/T1 Then I ran recon-all -stage1 -nomotioncor -subjid subjid and got: . . . Intensity Normalization Fri Jun 3 12:26:01 PDT 2005 $SUBJECTS_DIR/<subjid>/mri mri_normalize orig T1 reading from orig... normalizing image... talairach transform 0.712 0.146 -0.143 -13.113; -0.203 0.572 -0.426 -76.656; 0.026 0.448 0.590 151.306; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 Segmentation fault ERROR: mri_normalize exited with non-zero status ------------------------------------------ Then I did: recon-all -stage1 -nomotioncor -nuintensitycor -subjid subjid which also exited with non-zero status Then I did: recon-all -stage1 -nomotioncor -nonormalization -subjid subjid and got . . . white matter segmentation took 8.9 minutes writing output to wm... --------------------------------------------- Fill Fri Jun 3 13:25:01 PDT 2005 INFO: Uses mri/transforms/talairach.xfm mri_fill -xform transforms/talairach.xfm wm filled $SUBJECTS_DIR/subjid/mri INFO: Volume /tmp/mritotal_2558/nu_8_dxyz.mnc cannot be found. INFO: Using transforms/talairach.xfm and its offset for Talairach volume ... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.712 -0.143 -0.146 73.651; 0.026 0.590 -0.448 -51.272; 0.203 0.426 0.572 -67.608; 0.000 0.000 0.000 1.000; mri_fill: could not find valid seed for the cc No such file or directory Looking for area (min, max) = (350, 1400) area[0] = 15 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... Looking for area (min, max) = (350, 1400) area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... ERROR: mri_fill exited with non-zero status ------------------------------------------ Then I did recon-all -stage1 -lh-xyz -29.9 -45.8 162.2 -rh-xyz 36.2 -54.3 152.3 -cc-xyz -7.3 -68.4 188.9 -nomotioncor -nonormalization -subjid subjid and got . . . white matter segmentation took 8.9 minutes writing output to wm... --------------------------------------------- Fill Fri Jun 3 14:09:14 PDT 2005 INFO: Uses mri/transforms/talairach.xfm mri_fill -C -7.3 -68.4 188.9 -rh 36.2 -54.3 152.3 -lh -29.9 -45.8 162.2 -xform transforms/talairach.xfm wm filled $SUBJECTS_DIR/subjid/mri using Talairach position (-7, -68, 189) as corpus callosum seed point using Talairach position (36.2, -54.3, 152.3) as rh seed using Talairach position (-29.9, -45.8, 162.2) as lh seed INFO: Volume /tmp/mritotal_8012/nu_8_dxyz.mnc cannot be found. INFO: Using transforms/talairach.xfm and its offset for Talairach volume ... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.712 -0.143 -0.146 73.651; 0.026 0.590 -0.448 -51.272; 0.203 0.426 0.572 -67.608; 0.000 0.000 0.000 1.000; Segmentation fault ERROR: mri_fill exited with non-zero status ------------------------------------------ Any suggestions? Michele

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-notalairach option not working
by Margaret Duff 03 Jun '05

03 Jun '05

Hello, I am running the line recon-all-nmr -notalairach -stage1 -stage2 -subjid SM2C3 from SUBJECTS_DIR /space/troy/users/2/mikesfolder and in the std-env. The recon-all-nmr program is still creating a bad talairach transform that overwrites the good one I just made. So, the recon-all-nmr keeps exiting with errors because of the bad talairach. Is -notalairach still the correct option for not creating a transform during this step? Thanks, Margaret

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mri_normalize question
by Michele Perry 03 Jun '05

03 Jun '05

I'm trying to do a recon on a subject with a brain tumor. mri_normalize exited with non-zero status so -stage1 exited with errors. I tried running -stage1 with -usecontrolpoints (using 7 wm points) and it still failed. Then I tried running it with -nonormalization and got an error because there was no T1/COR-.info file. Then I tried running it with -nuintensitycor and it said that mri_normalize exited with nonzero status. Any ideas on how to get -stage1 to work? Michele

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morph_subject error
by Fornito, Alexander 03 Jun '05

03 Jun '05

Hi, I've come across some problems when I run morph_subject. It seems to work fine until near the end. I've included the final bit of the log below. The problem seems to occur after it calls MNI programs. I've been having trouble using the MNI tools through freesurfer, so I created the talairach.xfm separately and placed it in the transforms directory. Is this problem due to the trouble with the MNI tools? What are the MNI tools used for in morph_subject, and are they necessary at this step? Thanks again for your help, Alex registration took 1.70 hours writing registered surface to ../surf/lh.rh.sphere.reg... /data/flanders/work/alex/freesurfer/subjects/1000186_mni /data/flanders/work/alex/freesurfer/subjects/1000186_mni/scripts /data/flanders/work/alex/freesurfer/subjects/1000186_mni/scripts ------------------------------------- /data/flanders/work/alex/freesurfer/subjects/1000186_mni/scripts mris2rgb -o 1000186_mni.reg -both -c /data/flanders/work/alex/freesurfer/subjects/1000186_mni/surf/lh.sulc -canon /data/flanders/work/alex/freesurfer/subjects/1000186_mni/surf/lh.sphere.reg /data/flanders/work/alex/freesurfer/subjects/1000186_mni/surf/lh.sphere.reg /data/flanders/work/alex/freesurfer/subjects/1000186_mni/rgb ------------------------------------- using 1000186_mni.reg as output stem reading canonical coordinates from /data/flanders/work/alex/freesurfer/subjects/1000186_mni/surf/lh.sphere.reg. writing rgb file /data/flanders/work/alex/freesurfer/subjects/1000186_mni/rgb/lateral.lh.1000186_mni.reg.rgb writing rgb file /data/flanders/work/alex/freesurfer/subjects/1000186_mni/rgb/medial.lh.1000186_mni.reg.rgb morph_rgb-lh completed SUCCESSUFLLY ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.13 2004/02/02 18:24:58 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.12 2003/09/18 15:01:33 bert Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.4 2001/04/24 13:38:42 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects ERROR: cannot subject average7, needed to do average labels.

1 0

FreeSurfer and VBM data comparison
by Akemi Tomoda 02 Jun '05

02 Jun '05

Dear FS list, Here I have the FreeSurfer and the VBM data for the 26 young adults between the different parameters. I see that there is a Pearson's correlation of 0.9148 for the Left Hemisphere gmv between FS and VBM. For the right hemisphere there is a correlation of 0.9061. But when I compare the differences between the left and right hemispheres by FS and by VBM, I see that we get a negative correlation of -0.3806, p = 0.0551. And when we compare the laterality indices between the hemispheres for the 26 subjects from FS and VBM we get a correlation of -0.3464, p=0.0830. The mean (N=26) Left Hemisphere VBM data = 337820 (mm3) and for the Right Hemisphere it is 337020. With FreeSurfer we get Left Hemisphere = 363113 and for the Right Hemisphere = 368816. That is, with VBM the mean Left Hemisphere is larger than the right while with VBM the right hemisphere is the larger. The question for me is why is there a discrepancy on the differences between the hemispheres? Does this mean that FS and VBM are giving different data in spite of the strong correlations when comparing the individual hemispheres? This seems so to me. How do we account for this discrepancy in the face of the strong correlations between the FS and VBM results for the same hemisphere? Any suggestion or comments regarding this matter would be highly appreciated. Best, Akemi Developmental Biopsychiatry Research Program McLean Hospital, Belmont MA

2 1

GM segmentation
by Campbell, Zeke (NIH/NINDS) 02 Jun '05

02 Jun '05

Dear All: I would like to know which surface I should load on T1 volume to visualize cortical GM segmentation. Thanks. Zeke Campbell

2 1

Tutorial
by Michael Ryan Haynes 02 Jun '05

02 Jun '05

In FreeSurferTutorial.pdf, starting on page 27 for examples on correcting holes and handles, why do the images in the original bert file appear as right hemisphere on left while the images in the tutorial appear as right hemisphere on right side? Thanks.

1 0

skull stripping
by Fornito, Alexander 02 Jun '05

02 Jun '05

Hi all, The page about using FSL with freesurfer on the FSL website recommends using BET to skull strip the images before feeding them into freeusrfer. I've had a bit of play with this, and have noticed some marginal improvements. Would you generally recommed this practice? Are there any reasons not to? Also, what exactly does the -atlas option do? Thanks, Alex

2 1

pictures of MRI image segmentation
by Bagnato, Francesca (NIH/NINDS) 01 Jun '05

01 Jun '05

Hi: I am having troubles in preparing a picture showing MR image segmentation in the coronal, axial and sagittal planes. Any light on that? Thanks, --francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 31, 2005 1:50 PM To: Wan Park Cc: free surfer Subject: [Freesurfer] Re: Gray Volume question Hi Wan, they haven't been normalized. Typically you would normalize by the total intracranial volume, which can be a bit tricky to get from only a T1. If you normalize by total brain volume, that should be a bit more conservative, as it would normalize out total atrophy. cheers, Bruce On Tue, 31 May 2005, Wan Park wrote: > Hi, I have a question. I am getting the gray volume for a standard area > (G_subcallosal) in different brains (male and female) with different > conditions. > > If I want to compare these volumes, should I normalize them with the total > brain (or hemisphere) volume or can I use these results directly? I > understand that the FS fills the volume from a particular brain into a > standard brain. So, are the volumes already normalized? Thanks, > > Wan > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 5

occipatal cuts
by Joongnam Yang 31 May '05

31 May '05

Hi all, I did the occipital cut for the right brain and flattened it. When I opened it with Tksurfer of csurf, the flattened surface showed up on the right edge of the display window of Tksurfer, instead of being in the center of the window. (The left flattened surface came out in the center, and I did similarly for the left and right brains.). Has anyone had this problem? or how can I fix it? Thanks always for the great help that I get from this listing. Nam.

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