Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

Re: [Freesurfer] process volume again
by David Soscia 22 Aug '05

22 Aug '05

Thanks, after a little tweaking, I managed to get part of the process going. A few things I thought I would mention though... 1. At first when I tried to do the -nuintensitycor command it was saying it found no data in /mri (no orig.mgz file there). When I did mksubjdirs, it made folders for all of the steps (orig, T1, wm, brain, etc) And then when I did a conversion to mgz from dicom of my orig files, they went into my orig folder, ie. mri/orig/orig.mgz. Maybe I did the conversion wrong so it sent it there instead of in the mri directory, however I thought the purpose of the mksibjdirs was to make seperate folders to put the seperate steps into. After I saw this error message in the -nuintensitycor process, I moved the orig.mgz file from the orig directory into the mri directory and it worked fine. 2. When I run the next step, -normalization, I am getting an error half way through... [amc@amcpacs 1768-4]$ recon-all -subjid 1768-4 -normalization -mgz 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 $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### Using mgz format --------------------------------------------- Intensity Normalization Mon Aug 22 09:14:14 EDT 2005 /home/amc/freesurfer_new/freesurfer/subjects/1768-4/mri mri_normalize orig.mgz T1.mgz reading from orig.mgz... normalizing image... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 Segmentation fault ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Mon Aug 22 09:15:16 EDT 2005 Any ideas on what the problems could be? Thanks for your help so far. 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 >>> "Brian T. Quinn" <btquinn(a)nmr.mgh.harvard.edu> 08/20/05 3:49 PM >>> hi Dave- it sounds like you may be skipping some steps. what volume do you currently have? the order of the volumes to be created is: orig->nu->T1->brain->wm the -segmentation step only runs the brain->wm step. if you have an orig volume, use either: -stage1 or: -nuintensitycor -normalization -usenuintensitycor -skullstrip -segmentation stage one will take you a bit further down the FS stream, but will produce the wm volume. as for the -COR and -mgz flags, use whatever is appropriate. thanks, brian t. quinn On Fri, 19 Aug 2005, David Soscia wrote: > hey guys, > > Now I am getting this error when trying to process the volume: > > [amc@amcpacs 1768-4]$ recon-all -subjid 1768-4 -mgz -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 $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > ####################################### > Using mgz format > --------------------------------------------- > Segmentation Fri Aug 19 13:30:42 EDT 2005 > ERROR: cannot find brain.mgz > recon-all exited with errors at Fri Aug 19 13:30:42 EDT 2005 > > > i dont have a brain.mgz in the brain directory because I thought the > purpose of this process was to create it. Any suggestions? > > 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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: Welcome to the "Freesurfer" mailing list (Digest mode)
by Bosky Ravindranath 21 Aug '05

21 Aug '05

Hi, Does anybody know when the subcortical segmentation feature in Freesurfer is going to be released? Bosky

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libtk8.3.so error
by Bosky Ravindranath 21 Aug '05

21 Aug '05

I recently installed freesurfer on my Linux machine that runs RH9. When running tkmedit , I get the following error: tkmedit: error while loading shared libraries: libtk8.3.so: cannot open shared object file: No such file or directory I tried a solution posted to a simliar problem by downloading the lib files, but I got this message: rpm -i {tcl,tk}-8.3.2-1.i386.rpm package tcl-8.3.5-88 (which is newer than tcl-8.3.2-1) is already installed How do I get rid of this problem? Also, is the subcortical segmentation feature released in freesurfer-Linux-rh9-dev20050729.tar.gz? Regards, BR

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process volume again
by David Soscia 20 Aug '05

20 Aug '05

hey guys, Now I am getting this error when trying to process the volume: [amc@amcpacs 1768-4]$ recon-all -subjid 1768-4 -mgz -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 $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### Using mgz format --------------------------------------------- Segmentation Fri Aug 19 13:30:42 EDT 2005 ERROR: cannot find brain.mgz recon-all exited with errors at Fri Aug 19 13:30:42 EDT 2005 i dont have a brain.mgz in the brain directory because I thought the purpose of this process was to create it. Any suggestions? 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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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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