Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

using external usb hard drive with freesurfer
by Andrew H Bell 07 Jun '05

07 Jun '05

To all Has anyone had any experience using an external drive with freesurfer (under LINUX)? I am trying to use a FAT32 drive with Freesurfer (I also use this drive with XP) and I keep running into the following error: "First T1 image: /mnt/usb/afnidata/subjects/bert/mri/T1/COR-001 not found" However, when I check, the file is there but is listed in lower-case (i.e., "cor-001"). I cannot rename the file to upper-case - the file already exists... Is Freesurfer case-sensitive and if so, is there a way to tell it to look for lower-case filenames? Thanks Andy

3 2

RE: [Freesurfer] Missing libraries?
by Fornito, Alexander 06 Jun '05

06 Jun '05

Hi, We've managed to get it working. Your help is very much appeciated!! However, when I run recon-all -stage1, things work fine until it calls nu_correct. I then get a recurring message saying "Not implemented yet in cache_volume_range_has_changed()", before moving on to the next processing stage. Below is a sample of the output. Is this indicative of a problem? Thanks again, Alex Nu Intensity Correction Tue Jun 7 12:03:52 EST 2005 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:04:01] running: /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_14595/ nu/nu0.mnc nu/nu1.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() #...and so on... Number of iterations: 32 CV of field change: 0.000883872 [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:04:58] running: /usr/local/mni/bin/make_template -quiet -shrink 3 nu/nu0.mnc /var/tmp/nu_correct_14595//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done nu_correct -clobber nu/nu1.mnc nu/nu2.mnc [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:05:10] running: /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_15016/ nu/nu1.mnc nu/nu2.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 3 CV of field change: 0.000947262 [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:05:21] running: /usr/local/mni/bin/make_template -quiet -shrink 3 nu/nu1.mnc /var/tmp/nu_correct_15016//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done nu_correct -clobber nu/nu2.mnc nu/nu3.mnc [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:05:37] running: /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_15089/ nu/nu2.mnc nu/nu3.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 3 CV of field change: 0.000802066 [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:05:49] running: /usr/local/mni/bin/make_template -quiet -shrink 3 nu/nu2.mnc /var/tmp/nu_correct_15089//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done nu_correct -clobber nu/nu3.mnc nu/nu4.mnc [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:06:01] running: /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_15162/ nu/nu3.mnc nu/nu4.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 3 CV of field change: 0.000831802 [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:06:13] running: /usr/local/mni/bin/make_template -quiet -shrink 3 nu/nu3.mnc /var/tmp/nu_correct_15162//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done mri_convert nu/nu4.mnc nu mri_convert nu/nu4.mnc nu reading from nu/nu4.mnc... DimSizes: 3, 256, 256, 256, 1 DataType: 1 MINC Linear Transform -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000 -128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000 Done reading minc TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to nu... -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Sat 6/4/2005 7:41 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Missing libraries? Alex, I've just posted a source code bundle of most of the MNI-BIC tools, along with a Makefile for building/installing/testing this software. The README file is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README and the gzip file is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz Although the README says the ideal place to install is at /usr/pubsw/packages/mni/current, I've installed the set in a local home directory, and the segment_subject works for me (on Mac OS X, and Linux CENTOS 4) However, you may be able to get your existing install working by just adding the environment var DYLD_LIBRARY_PATH. See the README for an example. Your error (not finding a .so file) is indicative of this problem. Let me know how things go. Nick On Fri, 2005-05-27 at 14:38 +1000, Fornito, Alexander wrote: > Hi, > We're really stuck on this one... > We are running a linux kernel 2.4.26 debian 3.0 (woody). > We've installed the freesurfer and the packaged MINC tools in the apporpriate directories and set the appropriate environment variables. > We can't get the MNI tools to work through freesurfer, and only some limited MINC tools work if we try to run them on their own (eg., we can use MINC display, but can't do anyting with the images). It seems like there are some libraries missing (see below). Can you tell us why the MINC tools that came packaged with fressurfer aren't working? Is there something else that needs to be installed? > If I try to run mri_convert from the GUI after checking the MNI Linear > Register option in expert preferences, I get a message saying MNI align > not yet implemented. > If I run segment_subject I get : > > segment_subject 190 > cp: cannot stat > `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' > : No such file or directory > /data/flanders/work/alex/freesurfer/subjects/190/scripts > /data/flanders/work/ale > x/freesurfer/subjects > registering 190 > mri_convert orig orig/orig.mnc > reading from orig... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > writing to orig/orig.mnc... > mincinfo: error while loading shared libraries: libvolume_io.so.0: > cannot open shared object file: No such file or directory > Error executing mincinfo on orig/orig.mnc > Error: could not open file > "/data/flanders/work/alex/freesurfer/subjects/190/mr > i/transforms/talairach.xfm". > System message: No such file or directory > mri_add_xform_to_header: could not read xform file > '/data/flanders/work/alex/fre > esurfer/subjects/190/mri/transforms/talairach.xfm' > > Any help would be much appreciated!!! > Thanks, > Alex > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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RE: [Freesurfer] Missing libraries?
by Fornito, Alexander 05 Jun '05

05 Jun '05

Thanks Nick, We'll give it a try and keep you posted. A. -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Sat 6/4/2005 7:41 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Missing libraries? Alex, I've just posted a source code bundle of most of the MNI-BIC tools, along with a Makefile for building/installing/testing this software. The README file is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README and the gzip file is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz Although the README says the ideal place to install is at /usr/pubsw/packages/mni/current, I've installed the set in a local home directory, and the segment_subject works for me (on Mac OS X, and Linux CENTOS 4) However, you may be able to get your existing install working by just adding the environment var DYLD_LIBRARY_PATH. See the README for an example. Your error (not finding a .so file) is indicative of this problem. Let me know how things go. Nick On Fri, 2005-05-27 at 14:38 +1000, Fornito, Alexander wrote: > Hi, > We're really stuck on this one... > We are running a linux kernel 2.4.26 debian 3.0 (woody). > We've installed the freesurfer and the packaged MINC tools in the apporpriate directories and set the appropriate environment variables. > We can't get the MNI tools to work through freesurfer, and only some limited MINC tools work if we try to run them on their own (eg., we can use MINC display, but can't do anyting with the images). It seems like there are some libraries missing (see below). Can you tell us why the MINC tools that came packaged with fressurfer aren't working? Is there something else that needs to be installed? > If I try to run mri_convert from the GUI after checking the MNI Linear > Register option in expert preferences, I get a message saying MNI align > not yet implemented. > If I run segment_subject I get : > > segment_subject 190 > cp: cannot stat > `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' > : No such file or directory > /data/flanders/work/alex/freesurfer/subjects/190/scripts > /data/flanders/work/ale > x/freesurfer/subjects > registering 190 > mri_convert orig orig/orig.mnc > reading from orig... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > writing to orig/orig.mnc... > mincinfo: error while loading shared libraries: libvolume_io.so.0: > cannot open shared object file: No such file or directory > Error executing mincinfo on orig/orig.mnc > Error: could not open file > "/data/flanders/work/alex/freesurfer/subjects/190/mr > i/transforms/talairach.xfm". > System message: No such file or directory > mri_add_xform_to_header: could not read xform file > '/data/flanders/work/alex/fre > esurfer/subjects/190/mri/transforms/talairach.xfm' > > Any help would be much appreciated!!! > Thanks, > Alex > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Missing libraries?
by Fornito, Alexander 03 Jun '05

03 Jun '05

Hi, We're really stuck on this one... We are running a linux kernel 2.4.26 debian 3.0 (woody). We've installed the freesurfer and the packaged MINC tools in the apporpriate directories and set the appropriate environment variables. We can't get the MNI tools to work through freesurfer, and only some limited MINC tools work if we try to run them on their own (eg., we can use MINC display, but can't do anyting with the images). It seems like there are some libraries missing (see below). Can you tell us why the MINC tools that came packaged with fressurfer aren't working? Is there something else that needs to be installed? If I try to run mri_convert from the GUI after checking the MNI Linear Register option in expert preferences, I get a message saying MNI align not yet implemented. If I run segment_subject I get : segment_subject 190 cp: cannot stat `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' : No such file or directory /data/flanders/work/alex/freesurfer/subjects/190/scripts /data/flanders/work/ale x/freesurfer/subjects registering 190 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory Error executing mincinfo on orig/orig.mnc Error: could not open file "/data/flanders/work/alex/freesurfer/subjects/190/mr i/transforms/talairach.xfm". System message: No such file or directory mri_add_xform_to_header: could not read xform file '/data/flanders/work/alex/fre esurfer/subjects/190/mri/transforms/talairach.xfm' Any help would be much appreciated!!! Thanks, Alex

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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

3 2

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

1 0

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

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