Freesurfer October 2005

freesurfer@nmr.mgh.harvard.edu

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aseg
by antao＠itsa.ucsf.edu 27 Oct '05

27 Oct '05

Hi How to calculate the volume of segmented brain like hippocampus, subcortical nucleus? Thanks, Antao

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recalculating surfaces
by Dahlia Sharon 27 Oct '05

27 Oct '05

Hi, I overwrote several surface files (.inflated, .sulc, .curv, .smoothwm, .orig) by mistake while editing another subject. The volume in mri/wm/ is still the correct one. I should be able to run some of the recon steps again to get the correct surfaces back, but I don't want to do this without guidance so as not to make mistakes and start stepping over other files. Can you tell me which commands to run to regenerate these surfaces correctly? Thanks!!! Dahlia. PS - the subject is ~dahlia/structurals/subj21_bay2

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recon-all library dependencies
by James Voyvodic 27 Oct '05

27 Oct '05

I've upgraded to the latest development release (freesurfer-Linux-rh9-dev20051003-full.tar.gz) running on Linux Redhat 9 on an x86 platform. Recon-all crashes, apparently because of failed library dependencies, with the following message: /usr/local/mni/bin/volume_stats: /usr/lib/libstdc++.so.6: version `CXXABI_1.3' not found (required by /usr/local/mni/bin/volume_stats) /usr/local/mni/bin/volume_stats: /usr/lib/libstdc++.so.6: version `GLIBCXX_3.4' not found (required by /usr/local/mni/bin/volume_stats) nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux hawking 2.4.20-31.9 #1 Tue Apr 13 18:04:23 EDT 2004 i686 i686 i386 GNU/Linux recon-all exited with errors at Wed Oct 26 15:17:17 EDT 2005 It had previously crashed because it couldn't find libstdc++.so.6 at all, so I tried to appease it by using the old trick of linking libstdc++.so.5 to libstdc++.so.6, but obviously that wasn't enough. So the main question is: what libraries are needed to run the new version(s) of FreeSurfer? Is there a way to download the missing libraries from somewhere? When I installed and tried to run the most recent stable release (freesurfer-Linux-rh9-v2.1.tar.gz) I was foiled because I didn't have libtixwish installed, which is why I went to the development release that had more libraries. Yum says I have libstdc++ and doesn't offer a .so.6 variant. Do I need a different version of Linux? A side question: If recon-all crashes part way through, is there a way to skip the successful steps when restarting or does it have to redo all the steps in its autorecon (e.g. autorecon1) script? thanks, Jim ======================== James T. Voyvodic, Ph.D. Brain Imaging and Analysis Center Duke University Medical Center e-mail: jim.voyvodic(a)duke.edu

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converting thickess file to ascii
by Thomas, Adam (NIH/NIMH) 26 Oct '05

26 Oct '05

Can mris_convert be used to convert thickness files to ascii? My attempts so far have resulted in segfaults: [adamt@antimony surf]$ mris_convert lh.thickness lh.thickness.asc Segmentation fault [adamt@antimony surf]$ Or is there another way to convert thickness files to ascii? Thanks, -Adam --- Adam Thomas adamt(a)nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148

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re: good news and bad news (Bruce Fischl)
by Glenn Lawyer 26 Oct '05

26 Oct '05

Hi, Regarding Bruce's "GOOD NEWS" announcement from last friday: I wanted to thank Bruce, Doug, Nick, and everyone else on the dev. team for making FreeSurfer open source (also of course the folks Bruce mentioned: Anders, Howard, and Christian). I suspect that many of the people on this mailing list are not deeply into software issues, so perhaps you may not realize just how important opening up the source code is. I do know, however, that we are all committed to science. Science progresses much faster when ideas, results, and methods are shared in an open and unrestricted manner. So thanks again to the FreeSurfer team for sharing your hard-won knowledge with the rest of the world. +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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tkregister-sess errors
by Gold, Andrea 24 Oct '05

24 Oct '05

Hi all, I am having errors with the tkregister-sess command. I tried re-doing stages 1 & 2 of recon-all, but still get the same errors (see log window below)running the NMR standard environment on Kermit. It can't seem to open the structural even though the image files seem to be present in the structural directory (DCS_recon). Thanks!!!!! Functional data located in /space/phrenic/6/users/wright/studies/DCS Structural data located in /space/phrenic/6/users/wright/studies/DCS_recon [kermit:DCS] (nmr-std-env) tkregister-sess -sf sessid_all -df sessdir -------------------------------------------------------------- tkregister-sess logfile is /autofs/space/phrenic_006/users/wright/studies/DCS/log/tkregister-sess.log -------------------------------------------------------------- Session: /autofs/space/phrenic_006/users/wright/studies/DCS/dcs1.1 ---------------- Mon Oct 24 14:34:51 EDT 2005 INFO: anatdir set to /space/phrenic/6/users/wright/studies/DCS_recon//dcs1/mri/T1 ---------------------------------------------------- INFO: surface white does not exist for dcs1, so it will not be loaded into the display. This may be because the subject's anatomical data has not been processed with FreeSurfer in order to reconstruct the surface. You can change the surface from white with the -surf option (followed by the name of the surface. Continuing... ---------------------------------------------------- ________________________________________________ /autofs/space/phrenic_006/users/wright/studies/DCS/dcs1.1/bold/010 tkregister2 --targ /autofs/space/phrenic_006/users/wright/studies/DCS_recon/dcs1/mri/T1 --mov ./f bshort --reg ../register.dat --plane cor --title dcs1--dcs1.1--010 --volview targ ________________________________________________ target volume /autofs/space/phrenic_006/users/wright/studies/DCS_recon/dcs1/mri/T1 movable volume ./f reg file ../register.dat LoadVol 1 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.001 -0.002 -0.001 -1.863; -0.002 -1.001 -0.000 -91.365; 0.001 -0.000 1.001 -10.891; 0.000 0.000 0.000 1.000; float2int = 2 --------------------------------------- INFO: loading target /autofs/space/phrenic_006/users/wright/studies/DCS_recon/dcs1/mri/T1 INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ./f INFO: bvolumeRead: min = 0, max = 1295 INFO: changing move type to float Tmov: -------------------- -3.125 0.000 0.000 100.000; 0.000 0.000 3.300 -49.500; 0.000 -3.125 0.000 100.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 2 INFO: making tkreg matrix compatible with round ---- New registration matrix -------- 1.001 -0.001 -0.001 -0.304; -0.002 -1.001 -0.000 -93.078; 0.001 -0.000 1.001 -12.428; 0.000 0.000 -0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.001 -0.001 -0.001 -0.304; -0.002 -1.001 -0.000 -93.078; 0.001 -0.000 1.001 -12.428; 0.000 0.000 -0.000 1.000; subject = dcs1 Zoom Factor = 2 FOV = 256 Opening window dcs1

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Re: Freesurfer Digest, Vol 19, Issue 49
by Blaise Frederick 24 Oct '05

24 Oct '05

On Sep 27, 2005, at 3:06 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Message: 2 > Date: Tue, 27 Sep 2005 13:42:02 -0400 > From: Keith Schneider <ks(a)rcbi.rochester.edu> > Subject: [Freesurfer] mri_convert doesn't recognize DICOM files > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <1F6EBE81-3EC6-41F9-840C-1C2E8B4C05A6(a)rcbi.rochester.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > I installed Freesurfer on a G5 Tiger Mac, but mri_convert and > mri_parse_sdcmdir don't recognize my Siemens DICOM files (from a > Siemens Trio 3T) as DICOM files. Has anyone else encountered this? > > Other programs can read the DICOM files just fine. > > keith > > > ------------------------------ I have found exactly the same thing. The thing is, it _used_ to work... Using a G5 with 10.4.2, in a directory with DICOM files pulled off a Siemens Trio using Osirix, I execute the following: /usr/local/freesurfer/bin/Darwin/mri_convert -it dicom -ot analyze IM-0242-0001.dcm hoot I get the following error (many, many times) mri_convert(1841) malloc: *** Deallocation of a pointer not malloced: 0xd10ea0; This could be a double free(), or free() called with the middle of an allocated block; Try setting environment variable MallocHelp to see tools to help debug However, when all is said and done, I get a correct analyze file. The binary in question is: -rwxr-xr-x 1 frederic frederic 2034036 Feb 18 2004 /usr/local/ freesurfer/bin/Darwin/mri_convert However, if I execute: /Users/Shared/freesurfer/bin/mri_convert -it dicom -ot analyze IM-0242-0001.dcm hoot2 it returns with: no DICOM files found. Exit This binary is from the newest distribution that I have: -rwxr-xr-x 1 frederic wheel 6236540 Jul 7 21:23 /Users/Shared/ freesurfer/bin/mri_convert So it looks like something broke. Unfortunately, I don't want to just use the old binary, because it is missing many output formats (particularly nii) Blaise Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and/or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, PHI by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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RE: [Freesurfer] Anatomical parcellation in patients
by Bagnato, Francesca (NIH/NINDS) 21 Oct '05

21 Oct '05

Thanks Bruce, I was wondering if you have noted differences between 1.5 and 3T images as far as it concerns this issue. Indeed, the MS cortical lesions are definitely visible on a 3T anatomical RMI but barely detectable in 1.5T SPGRs. 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: Friday, October 21, 2005 7:39 PM To: Bagnato, Francesca (NIH/NINDS) Cc: Goulven Josse; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Anatomical parcellation in patients Hi Francesca, this is tough to answer as it depends on the exact location of the cortical lesion, and the thickness of the underlying white matter. As you know, we have done a fair number of MS subjects, so in general it's okay, but I can certainly imagine scenarios in which things fail. sorry I can't be more help. Bruce On Fri, 21 Oct 2005, Bagnato, Francesca (NIH/NINDS) wrote: > Dear Josse and all: > Before posing the parcellation problem with respect to patients with > cortical lesions, I was wondering to ask if anybody has a clue on how > the segmentation of the cortex/WM might work in patients with > juxtacortical/cortical lesions. > > In other words: how the drop of the signal given by cortical lesions > affects the segmentation of the cortex? Also, how much partial (CSF) > volume voxels due to the empty space left by cortical lesions may affect > the cortical thickness measurements? > > 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: Goulven Josse [mailto:goulven@uchicago.edu] > Sent: Friday, October 21, 2005 6:29 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: [Freesurfer] Anatomical parcellation in patients > > Dear freesurfers, > > We are trying to analyse data from patients who had an early stroke. > I did one automated parcellation (Fischl et al, 2004) in a patient with > a peri-ventricular enlargement associated with a large overall atrophy > of the injured hemisphere. I was pleased to find out that, even in the > injured hemisphere, the anatomy was -apparently- well parcellated. I am > now thinking of applying the parcellation to other subjects with a > similar lesion and, possibly, to subjects with a much bigger, cortical, > lesion. > > Before going ahead, I am wondering if anyone had an opinion about > whether it makes sense to use this parcellation in patients, while it > was (i think) originally designed for normal brains. Variability is > huge in normals but still ... > > thanks ! > Goulven Josse > (Brain Research Imaging Center, U of Chicago) > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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RE: [Freesurfer] Anatomical parcellation in patients
by Bagnato, Francesca (NIH/NINDS) 21 Oct '05

21 Oct '05

Dear Josse and all: Before posing the parcellation problem with respect to patients with cortical lesions, I was wondering to ask if anybody has a clue on how the segmentation of the cortex/WM might work in patients with juxtacortical/cortical lesions. In other words: how the drop of the signal given by cortical lesions affects the segmentation of the cortex? Also, how much partial (CSF) volume voxels due to the empty space left by cortical lesions may affect the cortical thickness measurements? 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: Goulven Josse [mailto:goulven@uchicago.edu] Sent: Friday, October 21, 2005 6:29 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Anatomical parcellation in patients Dear freesurfers, We are trying to analyse data from patients who had an early stroke. I did one automated parcellation (Fischl et al, 2004) in a patient with a peri-ventricular enlargement associated with a large overall atrophy of the injured hemisphere. I was pleased to find out that, even in the injured hemisphere, the anatomy was -apparently- well parcellated. I am now thinking of applying the parcellation to other subjects with a similar lesion and, possibly, to subjects with a much bigger, cortical, lesion. Before going ahead, I am wondering if anyone had an opinion about whether it makes sense to use this parcellation in patients, while it was (i think) originally designed for normal brains. Variability is huge in normals but still ... thanks ! Goulven Josse (Brain Research Imaging Center, U of Chicago) _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Anatomical parcellation in patients
by Goulven Josse 21 Oct '05

21 Oct '05

Dear freesurfers, We are trying to analyse data from patients who had an early stroke. I did one automated parcellation (Fischl et al, 2004) in a patient with a peri-ventricular enlargement associated with a large overall atrophy of the injured hemisphere. I was pleased to find out that, even in the injured hemisphere, the anatomy was -apparently- well parcellated. I am now thinking of applying the parcellation to other subjects with a similar lesion and, possibly, to subjects with a much bigger, cortical, lesion. Before going ahead, I am wondering if anyone had an opinion about whether it makes sense to use this parcellation in patients, while it was (i think) originally designed for normal brains. Variability is huge in normals but still ... thanks ! Goulven Josse (Brain Research Imaging Center, U of Chicago)

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Freesurfer October 2005