Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Fwd: Re: [Freesurfer] mri_watershed
by Sasha Wolosin 19 Aug '05

19 Aug '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_watershed
by Sasha Wolosin 19 Aug '05

19 Aug '05

We use an anatomical analysis program called Brain Image in our lab. We would like to speed up our analysis in Brain Image by replacing manual skull stripping with FreeSurfer's automated skull strip program. For this we would need to do a skull strip alone, without adjusting intensity values or contrast. Is this possible? Is this a reasonable thing to do? I have run mri_watershed with the input from orig on several subjects, and the output volume looks much brighter than the orig volume. Does mri_watershed normalize intensities or change the contrast in order to strip the skull? 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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segmentation fault during mri_convert
by Margaret Duff 19 Aug '05

19 Aug '05

Hi, Is mri_convert setup yet to convert to mgz format? I have been trying it in both the std and dev environment from dicom format and spm format and i keep getting a segmentation fault. it still converts to cor format fine but i thought we were trying to get away from that. i dont know exactly whats causing it, but here is my command line and the running information. troy:mduff[84] mri_convert -ot mgz -it dicom 33749275 $SUBJECTS_DIR/SM2C1_autoreconall/mri/orig/002 mri_convert -ot mgz -it dicom 33749275 /space/troy/1/users/FREESURFER/SM2C1_autoreconall/mri/orig/002 reading from 33749275... Getting Series No Scanning Directory INFO: Found 131 files in /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028 INFO: Scanning for Series Number 28 INFO: found 128 files in series INFO: loading series header info. INFO: sorting. RunNo = 27 INFO: (256 256 128), nframes = 1, ismosaic=0 FileName /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028/33747925 Identification NumarisVer syngo MR 2004V 4VB11D ScannerModel Avanto PatientName sm2c1 Date and time StudyDate 20041118 StudyTime 180537.015000 SeriesTime 190942.968000 AcqTime 190056.292500 Acquisition parameters PulseSeq tfl3d1_ns Protocol T1_MPRAGE_sag PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.31 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 27 SeriesNo 28 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 71.7733 130.0894 131.5385 VolRes 1.0000 1.0000 1.3300 VolDim 256 256 128 Vc 0.1238 -0.9687 -0.2150 Vr -0.0454 0.2110 -0.9764 Vs -0.9913 -0.1306 0.0178 VolCenter -2.5670 21.9742 -19.4516 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). 128 DICOM 3.0 files in list Found 128 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 128. reading DICOM image... ------------------------------------------------- DICOM meta-header file name /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028/33747925 Date and time study date 20041118 study time 180537.015000 series time 190942.968000 acquisition time 190942.968000 Identification patient name sm2c1 manufacturer SIEMENS Dimensions number of rows 256 number of columns 256 number of frames 128 pixel width 1 pixel height 1 slice thickness 1.33 field of view 256 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 3.31 repetition time 2730 inversion time 1000 echo number 0 flip angle 0.122173 bits allocated 16 Spatial information first image position -71.7733 -130.089 131.539 last image position 95.662 -108.024 134.554 image orientation -0.123794 0.968728 -0.215038 0.0453834 -0.210951 -0.976442 ------------------------------------------------- TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (0.123794, -0.968728, -0.215038) j_ras = (-0.0453834, 0.210951, -0.976442) k_ras = (-0.99127, -0.130637, 0.0178497) writing to /space/troy/1/users/FREESURFER/SM2C1_autoreconall/mri/orig/002... Segmentation fault i saw a couple other problems on the list but nothing exactly like this. thanks for the help. margaret

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new freesurfer atlases for dev
by Doug Greve 19 Aug '05

19 Aug '05

For those in the NMR center using the freesurfer dev environment, there will re a change in recon-all to use "new" atlaes by default. This change will be live on Monday. The new cortical atlases are based on automatically filling ventricles and subcortical structures using the automatic subcortical segmentations (asegs). This is part of the "autorecon" stream accessed with the -autorecon flags (ie, -autorecon-all, -autorecon1, etc). The new subcortical atlas is based on 40 subjects. To continue to use the old atlases, run recon-all with -old-atlas. If you use any of the "stage" flags (ie, -all, -stage1, -stage2, etc), recon-all will automatically use the old atlases to maintain consistency. Specifications of individual steps (eg, -surfreg) will use the new atlases. To help keep track of which atlases were used, recon-all now stores he names of the atlases used for a subject in the following files located in the subject's scripts directory: mri_em_register.atlas.dat - subcortical atlas (new=RB40_talairach_2005-07-20.gca, old=talairach_mixed.gca) mris_register.atlas.dat - cortical registration atlas (new=average.curvature.filled.buckner40.tif, old=average.tif) mris_ca_label.atlas.dat - cortical label atlas (new=curvature.buckner40.filled.desikan_killiany.gcs, old=atlas2002_simple.gcs) If these files do not exist, then the old atlases are implied. doug -- 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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Permission denied
by Arvind Gururajan 19 Aug '05

19 Aug '05

Hello, Recently moved freesurfer from one system to another, but I am having trouble executing it. ./csurf: Permission denied. I have license in the right folder. Has anyone experienced the same problem. Thanks, Arvind

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coregistration
by antao＠itsa.ucsf.edu 19 Aug '05

19 Aug '05

I always have a problem to coregistrate T1 images to Talairach, Is there any way to improve the accuracy of coregistration besides tkregister2? Thanks, Antao

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process volume
by David Soscia 19 Aug '05

19 Aug '05

hey guys, Im trying to process an orig scan from the terminal line: [amc@amcpacs orig]$ recon-all -subjid 1768-4 -segmentation INFO: SUBJECTS_DIR is /home/amc/freesurfer_new/freesurfer/subjects ######################################## program versions used $Id: recon-all-nmr,v 1.72 2005/07/12 15:56:32 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin 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 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 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 $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### ~/freesurfer_new/freesurfer/subjects/1768-4 Using COR format --------------------------------------------- Segmentation Thu Aug 18 14:30:56 EDT 2005 ERROR: cannot find brain/COR-.info recon-all exited with errors at Thu Aug 18 14:30:56 EDT 2005 Notice how it says "using COR format." The file I am trying to convert is in mgz format, using the new freesurfer version. I'm confused as to why it is doing this. Thanks, Dave David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad(a)mail.amc.edu

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mgz conversion
by David Soscia 18 Aug '05

18 Aug '05

hey guys, When I go to do a conversion from dicom to mgz, im getting the error: mri_convert -ot mgz Image0001.dcm . mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory I did an ls command for this file and found no matches in my /usr/local/lib or /usr/lib directories. I'm guessing this means I need to install the proper libraries. I'm fairly new to Linux, so I don't know how to go about doing this. Any ideas? Thanks Dave David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad(a)mail.amc.edu

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Re: [Freesurfer] mgz conversion
by Rudolph Pienaar 18 Aug '05

18 Aug '05

I should have mentioned as a double check that you can type the following: rpm -qa | grep gsl to see if any 'rpm' (the package management system) files installed on your system match the gsl. Probably you won't find anything. The easiest way to install software for a RedHat system is to use 'rpm' files. I have added 'rpm' files for the gsl libraries to the Martinos Center's "File Drop" application. This app will send you an automatic email with instructions how to download these files (you should have received the notification by now). Follow the instructions you've received and download the files (there are two - gsl-devel-1.5-1.i386.rpm and gsl-1.5-1.i386.rpm) to your local box. OK - for the following, I'm assuming that you have root access to your local machine. Change to the root user: su - (and enter the root password). Change to the directory where you downloaded the gsl rpm files. Say you downloaded them to /tmp: cd /tmp Now install them with rpm -Uhv *.rpm and you'll see a short report as each rpm is installed. You should be all set now. Good luck, -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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using Freesurfer with external storage media
by Glenn Lawyer 17 Aug '05

17 Aug '05

Hi, I remeber a discussion here a month or so back about using Freesurfer with USB hard drives. People were having problems because the hard drive changed file names to lower case (i.e. cor instead of COR). The solution posted to the list was a script that would rename all cor files to uppercase. There is an easier way. You can reformat the drive with an ext3 file system. Ext3 is the (default) Linux file system, and provides support for case-sensitive file names (as well as permissions, links, etc). So once re-formatted you will no longer have the re-naming problem. Two warnings. 1) Reformatting will destroy ALL data on the drive; be prepared before you do this. 2) Windows cannot read ext3 file systems. Reformatting will make your drive unreadable to any Windows-based machine. To do it, as root: umount /media/usbharddisk # make sure the drive is not mounted mke2fs -j [device /dev] # reformat drive where [device /dev] is the link in the /dev directory where the drive is located. It should be something like /dev/sda1 or /dev/sdb1. You can tell by looking at the output of dmesg. Look for a section like this: -------------------- begin terminal output --------------------------- user@machine $ dmesg .......... usb 1-4: new high speed USB device using ehci_hcd and address 3 Initializing USB Mass Storage driver... scsi2 : SCSI emulation for USB Mass Storage devices usb-storage: device found at 3 usb-storage: waiting for device to settle before scanning usbcore: registered new driver usb-storage USB Mass Storage support registered. Vendor: Maxtor Model: OneTouch Rev: 0201 Type: Direct-Access ANSI SCSI revision: 00 SCSI device sdb: 490232832 512-byte hdwr sectors (250999 MB) sdb: assuming drive cache: write through SCSI device sdb: 490232832 512-byte hdwr sectors (250999 MB) sdb: assuming drive cache: write through sdb: sdb1 <---- LOOK HERE Attached scsi disk sdb at scsi2, channel 0, id 0, lun 0 usb-storage: device scan complete ----------------------------end terminal output------------------ The key line is sdb: sdb1 , which tells me that my disk is linked via sdb1, so to reformat I type mke2fs -j /dev/sdb1 +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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