Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Inflate from original surface files
by Arvind Gururajan 09 Jun '05

09 Jun '05

Hello, We have already generated a number of original surface files (.orig) in our lab. We were wondering if there is a way to generate the smooth and the inflated surface from the existing .orig files? Could you provide us a seperate tool to do this conversion? Sincerely, Arvind Gururajan

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RE: [Freesurfer] recon-all-nmr -disable-autoseg
by Fornito, Alexander 08 Jun '05

08 Jun '05

I can't find any usage or help for parcellate_subject, and if I simply run parcellate_subject [subjname], I get the following message: CSURF_DIR: Undefined variable. Any clues? Thanks, A. -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thu 6/9/2005 1:10 AM To: Bruce Fischl Cc: Fornito, Alexander; Elizabeth Fenstermacher; freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg I think it looks in the average7 directory for a few labels (central sulc, calc, ...), then maps them to your subject through the registration. The intent was that you could then look at these labels to make sure they were in about the right place. doug Bruce Fischl wrote: > the labels are deprecated since we have the cortical parcellation. And > yes, run parcellate_subject and it will create *.annot files in the > label dir. > cheers, > Bruce > > On Wed, 8 Jun 2005, Fornito, Alexander wrote: > >> That worked, thanks, Doug. >> To expand on the labels issue, from my understanding, the labels are >> used to check that the registration worked, and that these are >> automatically created. >> I don't have any files in my labels directory. >> Do you need to run parcellate_subject to get them? >> Is there any documentation on parcellate_subject? I tried to run it >> and got the message: >> CSURF_DIR: Undefined variable. >> >> as an aside, where is the average7 surface. I though it might be in >> /usr/local/freesurfer/average/, but I don't seem to be able to open >> any of the files in there with tksurfer. >> Thanks again, >> Alex >> >> >> >> -----Original Message----- >> From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] >> Sent: Wed 6/8/2005 11:08 AM >> To: Elizabeth Fenstermacher >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg >> use the one in dev not std env >> >> >> Elizabeth Fenstermacher wrote: >> >>> >>> Hello All, >>> >>> I have a number of jobs that I will be running through recon-all-nmr >>> -stage1 in the next few days. I tried using the -disable-autoseg >>> flag, but it seems not to work as the jobs I submitted this morning >>> have now run for 50 minutes. >>> >>> The command line as I typed it was >>> >>> pbsubmit -c "recon-all-nmr -stage1 -subjid $s -nuintensitycor >>> -usenuintensitycor -disable-autoseg" >>> >>> perhaps I've misplaced the flag? If anyone has any insight as to why >>> it seems to be persitting in running the autoseg I would appreciate it. >>> >>> Thanks! >>> Eliz >>> _______________________________________________ >>> 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

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freesurfer course
by Kerr, Catherine E. 08 Jun '05

08 Jun '05

Someone told me there was going to be a freesurfer course at the NMR center in July. Is it possible to register? Who would have this information? Thanks

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RE: [Freesurfer] recon-all-nmr -disable-autoseg
by Fornito, Alexander 08 Jun '05

08 Jun '05

That worked, thanks, Doug. To expand on the labels issue, from my understanding, the labels are used to check that the registration worked, and that these are automatically created. I don't have any files in my labels directory. Do you need to run parcellate_subject to get them? Is there any documentation on parcellate_subject? I tried to run it and got the message: CSURF_DIR: Undefined variable. as an aside, where is the average7 surface. I though it might be in /usr/local/freesurfer/average/, but I don't seem to be able to open any of the files in there with tksurfer. Thanks again, Alex -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Wed 6/8/2005 11:08 AM To: Elizabeth Fenstermacher Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg use the one in dev not std env Elizabeth Fenstermacher wrote: > > Hello All, > > I have a number of jobs that I will be running through recon-all-nmr > -stage1 in the next few days. I tried using the -disable-autoseg > flag, but it seems not to work as the jobs I submitted this morning > have now run for 50 minutes. > > The command line as I typed it was > > pbsubmit -c "recon-all-nmr -stage1 -subjid $s -nuintensitycor > -usenuintensitycor -disable-autoseg" > > perhaps I've misplaced the flag? If anyone has any insight as to why > it seems to be persitting in running the autoseg I would appreciate it. > > Thanks! > Eliz > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon-all-nmr -disable-autoseg
by Elizabeth Fenstermacher 07 Jun '05

07 Jun '05

Hello All, I have a number of jobs that I will be running through recon-all-nmr -stage1 in the next few days. I tried using the -disable-autoseg flag, but it seems not to work as the jobs I submitted this morning have now run for 50 minutes. The command line as I typed it was pbsubmit -c "recon-all-nmr -stage1 -subjid $s -nuintensitycor -usenuintensitycor -disable-autoseg" perhaps I've misplaced the flag? If anyone has any insight as to why it seems to be persitting in running the autoseg I would appreciate it. Thanks! Eliz

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recon-all stage4b error
by Fornito, Alexander 07 Jun '05

07 Jun '05

Hi all, I've created my the fional surface for some people and am trying to register them using recon-all -stage4b.However, I get an error message saying that I needed to do average labels (see output below). I've noticed that I get the same message if I try to morph_subject, except morph_subject actually creates sphere.reg files. Am I missing something? Thanks for your patience! Alex recon-all -subjid 186 -stage4b ######################################## 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/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ $Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects ERROR: cannot subject average7, needed to do average labels.

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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

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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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