Freesurfer August 2005

freesurfer@nmr.mgh.harvard.edu

42 participants
72 discussions

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

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documentation of matrix format for talairach transform
by Tracy Wang 31 Aug '05

31 Aug '05

Hi all, I was wondering if anyone knows what the format of the matrix in the talairach.xfm file is or if there is any documentation available describing the matrix format. Thanks! Tracy Wang Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

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ERROR: MRISeqchangeType
by Daniel Goldman 31 Aug '05

31 Aug '05

I recently received an error I've never seen before at the very end of a call to mri_convert: INFO: set hdr.hist.orient to 'coronal flipped' mri_convert -ot spm -rl /space/windu/4/users/recon//ESWJ78_recon/mri/orig/ /space/windu/4/users/recon//ESWJ78_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz /space/windu/4/users/recon//ESWJ78_recon/mri/32echo/magnitude/t2star_imgs/t2star_params.img reading from /space/windu/4/users/recon//ESWJ78_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.00513606, -0.981282, 0.192508) j_ras = (-0.0277379, -0.192297, -0.980945) k_ras = (-0.999602, 0.010378, 0.026231) reading template info from volume /space/windu/4/users/recon//ESWJ78_recon/mri/orig/... changing data type from 3 to 0 (noscale = 0)... MRIchangeType: Building histogram ERROR: MRISeqchangeType Any idea as to what the problem might be? Thanks very much, - Daniel Goldman

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OSX or linux for new FS?
by Fred Dick 30 Aug '05

30 Aug '05

Hi Bruce, Doug, et al. I was going to pick up some machines for freesurfer recon purposes - any recommendations on preferred platform? cheers, Fred

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Recon-all followup
by Clifford A. Smith, PhD 30 Aug '05

30 Aug '05

Following Yuan-Fen Kuo¹s suggestion, I added a # at line 275 in recon-all. Recon-all stage1 now proceeds until it crashes with the following: Intensity Normalization Tue Aug 30 12:47:03 CDT 2005 /Users/Shared/freesurfer/subjects/00139/mri mri_normalize orig.mgz T1.mgz reading from orig.mgz... normalizing image... talairach transform 1.131 -0.045 -0.066 0.052; 0.052 1.009 0.210 -10.266; 0.056 -0.234 1.111 -12.367; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 Bus error ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Tue Aug 30 12:48:33 CDT 2005 Any suggestions on proceeding? ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

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converting from ANALYZE 2D format
by Renat Yakupov 30 Aug '05

30 Aug '05

Can FreeSurfer read from ANALYZE 7.5 2D images? I have some brain volumes saved as 2D, a file per each slice. I can probably combine then into a single 3D volume in SPM or something, but I was wondering if FreeSurfer can read them in directly in this form? Thanks. Regards, Renat.

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Recon-all question
by Clifford A. Smith, PhD 30 Aug '05

30 Aug '05

I¹ve installed Freesurfer on Mac running Tiger. Am able to run mri_convert to attain 001.mgz and view with tkmedit without a problem. Can run recon-all help and attain the help files, but running recon-all subjid <subject name> -all (or autorecon1) mgz does not produce any image output only the following: Any suggestions? Thanks. Cliff % [Clifford-Smiths-Computer:shared/freesurfer/subjects] Cliff% recon-all -subjid 00139 -autorecon1 -mgz INFO: SUBJECTS_DIR is /Users/Shared/freesurfer/subjects ######################################## program versions used $Id: recon-all-nmr,v 1.71 2005/07/11 22:46:53 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve 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 $ !p$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 1.7 2004/08/31 18:07:37 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 $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### Using mgz format . ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

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mgz format
by Sasha Wolosin 29 Aug '05

29 Aug '05

Sorry to send this twice, but I should have elaborated: I am trying to convert files to mgz format. I was able to run mri_convert, but when I run csurf and attempt to open the orig volume, I get the error: "First orig image: /freesurfer/subjects/2332/mri/orig/COR-001 not found" Does anyone know why this may happen? Here is the command and output: [root@localhost /freesurfer]# cd subjects/2332/mri/orig [root@localhost orig]# ls 2332_analyze 2332_crsg [root@localhost orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz reading from 2332_crsg/001... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image... ------------------------------------------------- DICOM meta-header file name 2332_crsg/001 Date and time study date 20030630 study time 101639.0000 series time 104735.12 acquisition time 104735.12 Identification patient name ... manufacturer Philips Medical Systems Dimensions number of rows 256 number of columns 256 number of frames 124 pixel width 0.9375 pixel height 0.9375 slice thickness 1.5 field of view 240 image number 1 (might be not reliable) Acquisition parameters echo time 6.00003 repetition time 35 inversion time not found echo number 1 flip angle 0.785398 bits allocated 16 Spatial information first image position -114.756 -101.936 133.356 last image position -126.115 82.1994 135.698 image orientation 0.998088 0.0614863 0.00638348 0.00559035 0.0130627 -0.999899 ------------------------------------------------- TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to 001.mgz... [root@localhost orig]# csurf 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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Re: [Freesurfer] Re: new Freesurfer version
by Sasha Wolosin 29 Aug '05

29 Aug '05

I ran mri_convert with the input as the folder name followed by / and that seems to be working fine, but when I run csurf I still get the same error, and when I run tkmedit I get the error below: [root@localhost /freesurfer]# mri_convert -it dicom -ot mgz /freesurfer/subjects/2333/mri/orig/2333_crsg/ /freesurfer/subjects/2333/mri/orig/001.mgz mri_convert -it dicom -ot mgz /freesurfer/subjects/2333/mri/orig/2333_crsg/ /freesurfer/subjects/2333/mri/orig/001.mgz reading from /freesurfer/subjects/2333/mri/orig/2333_crsg/... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image... ------------------------------------------------- DICOM meta-header file name /freesurfer/subjects/2333/mri/orig/2333_crsg/001Date and time study date 20030617 study time 153907.0000 series time 155302.26 acquisition time 155302.26 Identification patient name Little,Britney manufacturer Philips Medical Systems Dimensions number of rows 256 number of columns 256 number of frames 124 pixel width 0.9375 pixel height 0.9375 slice thickness 1.5 field of view 240 image number 1 (might be not reliable) Acquisition parameters echo time 6.00003 repetition time 35 inversion time not found echo number 1 flip angle 0.785398 bits allocated 16 Spatial information first image position -127.793 -89.0762 120.125 last image position -113.357 94.0528 137.314 image orientation 0.996907 -0.0785857 5.7501e-10 0.00732152 0.0928779 -0.995651 ------------------------------------------------- TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.996907, 0.0785857, 5.7501e-10) j_ras = (-0.00732152, -0.0928779, -0.995651) k_ras = (-0.0782441, -0.992571, 0.0931655) writing to /freesurfer/subjects/2333/mri/orig/001.mgz... [root@localhost /freesurfer]# csurf csurf: logfile: /freesurfer/subjects/2333/scripts/csurf.log [root@localhost /freesurfer]# tkmedit 2332 orig Reading /freesurfer/lib/tcl/tkm_common.tcl Reading /freesurfer/lib/tcl/tkm_wrappers.tcl [root@localhost /freesurfer]# tkmedit 2333 orig corRead(): can't open file /freesurfer/subjects/2333/mri/orig/COR-.info Error: Loading volume orig Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. [root@localhost /freesurfer]# Thanks, Sasha >> Jenni Pacheco <jpacheco(a)nmr.mgh.harvard.edu> 08/29/05 5:24 PM >>> Hi Sasha, try this as your mri_convert command, see if it works: mri_convert -it dicom -ot mgz 2332_crsg/ 001.mgz Jenni On Mon, 29 Aug 2005, Sasha Wolosin wrote: > Here is the full command and output > When I try to open the orig volume, I get the error: > "First orig image: > /freesurfer/subjects/2332/mri/orig/COR-001 not found" > > [root@localhost /freesurfer]# cd subjects/2332/mri/orig > [root@localhost orig]# ls > 2332_analyze 2332_crsg > [root@localhost orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz > mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz > reading from 2332_crsg/001... > 124 DICOM 3.0 files in list > Found 124 DICOM Files > WARNING: NumberOfFrames 0 != Found Count of slices 124. > reading DICOM image... > ------------------------------------------------- > DICOM meta-header > > file name 2332_crsg/001 > Date and time > study date 20030630 > study time 101639.0000 > series time 104735.12 > acquisition time 104735.12 > Identification > patient name ... > manufacturer Philips Medical Systems > Dimensions > number of rows 256 > number of columns 256 > number of frames 124 > pixel width 0.9375 > pixel height 0.9375 > slice thickness 1.5 > field of view 240 > image number 1 (might be not reliable) > Acquisition parameters > echo time 6.00003 > repetition time 35 > inversion time not found > echo number 1 > flip angle 0.785398 > bits allocated 16 > Spatial information > first image position -114.756 -101.936 133.356 > last image position -126.115 82.1994 135.698 > image orientation 0.998088 0.0614863 0.00638348 0.00559035 0.0130627 -0.999899 > ------------------------------------------------- > > TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 > i_ras = (-0.998088, -0.0614863, 0.00638348) > j_ras = (-0.00559035, -0.0130627, -0.999899) > k_ras = (0.0615663, -0.998022, 0.0126937) > writing to 001.mgz... > [root@localhost orig]# csurf > > Thanks, > Sasha > > > > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 >Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 08/29/05 4:50 PM >>> > p.s. in general please include the full command line and output, > otherwise it's really hard to help you. Also, if you send these things to > the freesurfer list your response time will get a lot better as there are > a bunch of people who answer questions on it > > On Mon, 29 Aug 2005, Sasha Wolosin wrote: > >> Hi Nick, >> >> We now have the libraries installed, and we have managed to get freesurfer running on FC4, and I am able to convert from dicom to COR by typing: >> mri_convert -it dicom -ot cor 2332_crsg/001 001 >> >> but I am having trouble converting to/ opening files in mgz format. When I specify the output type as mgz instead of cor, I get a "segmentation fault" and when I try to open the orig volume in csurf I get the error: >> "First orig image: >> /freesurfer/subjects/2332/mri/orig/COR-001 not found" >> >> Is this version of freesurfer not set up to use mgz files yet? Or is there some setting I must change? >> >> Thanks, >> Sasha >> >> >> >> Sasha Wolosin >> Research Assistant >> Developmental Cognitive Neurology >> Kennedy Krieger Institute >> 707 N. Broadway >> Baltimore, MD 21205 >> ph: (443) 923-9270 >>>>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 08/24/05 4:15 PM >>> >> Sasha, >> >> Hi, Freesurfer requires the following libraries, which are sometimes >> (and sometimes not) included in Linux distributions: >> >> tcl, tk, tix, blt, gsl, tiff, jpeg, and glut >> >> Usually, a sysadmin will install these, but we are finding that a lot of >> people do not have the tcl/tk/tix/blt tools installed and working (and >> that work well with freesurfer). >> >> So for now, you will need to install the tcl/tk/tix/blt tools. Or you >> can try downloading a source code bundle, called fs_supportlibs.tar.gz >> from our distribution site: >> >> http://www.bic.mni.mcgill.ca/software/distribution/ >> >> to untar/unzip, type: >> >> tar zxvf fs_supportlibs.tar.gz >> >> then type >> >> cd fs_supportlibs >> setenv LIBS_DIR /usr >> >> then to build tcl and tk: >> >> ./build-tcltk.csh >> >> and tix and blt: >> >> ./build-tix.csh >> ./build-blt >> >> Upon completion, you should see the libs in the /usr/lib directory. >> I can't guarantee this will work well for you, some build engineer >> skills are required if problems are encountered. You may want to have >> your sysadmin do it. >> >> We are considering including some of these libs in the next release. >> >> As for not finding the nu_correct command, this seems to be more basic >> problem. Are the installed MINC tools in your path? type: >> >> echo $PATH >> >> and look for /usr/pubsw/packages/mni/current/bin >> >> the SetUpFreeSurfer.csh script sets this up. >> >> Nick >> >> >> On Wed, 2005-08-24 at 10:51 -0400, Sasha Wolosin wrote: >>> Hi Nick, >>> Thanks for the quick response. I downloaded the binaries from the distribution site (mni-Linux-centos4-v1.4.tar.gz) and I untarred the files to the /usr folder on my hard drive. I no longer get an error from the set up file, but freesurfer doesn't seem to be working properly. I am working with FC4, which we have recently installed and have not used yet, so I don't know if this could be a problem with our FC4 installation. Here's what I get when I run the set up and type some commands: >>> >>> [root@localhost /freesurfer]# tcsh >>> [root@localhost /freesurfer]# source MySetUpFreeSurfer.csh >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> FREESURFER_HOME /freesurfer >>> FSFAST_HOME /freesurfer/fsfast >>> SUBJECTS_DIR /freesurfer/subjects >>> FUNCTIONALS_DIR /freesurfer/sessions >>> MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin >>> MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib >>> PERL5LIB /usr/pubsw/packages/mni/current/lib/perl5/5.8.5 >>> QTDIR /usr/lib/qt-3.3 >>> [root@localhost /freesurfer]# csurf >>> /freesurfer/bin//csurf: line 4: /usr/bin/tixwish: No such file or directory >>> /freesurfer/bin//csurf: line 4: exec: /usr/bin/tixwish: cannot execute: No such file or directory >>> [root@localhost /freesurfer]# nu_correct >>> nu_correct: Command not found. >>> [root@localhost /freesurfer]# tkmedit >>> tkmedit: error while loading shared libraries: libtix8.1.8.4.so: cannot open shared object file: No such file or directory >>> [root@localhost /freesurfer]# >>> >>> Thanks, >>> Sasha >>> >>> >>> Sasha Wolosin >>> Research Assistant >>> Developmental Cognitive Neurology >>> Kennedy Krieger Institute >>> 707 N. Broadway >>> Baltimore, MD 21205 >>> ph: (443) 923-9270 >>>>>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 08/23/05 6:32 PM >>> >>> Sasha, >>> >>> The MINC tools are not included in the freesurfer Linux download. >>> These tools are a whole can of worms unto themselves, at least in >>> terms of installation and integration with freesurfer, but there are >>> three possibilities to get these tools: >>> >>> 1) get the binaries from the main MNI site: >>> http://www.bic.mni.mcgill.ca/software/distribution/ >>> >>> you will need the NetCD, MINC and BICPL packages. I cannot say with >>> certainty whether this will work with FreeSurfer, as we have built all >>> the necessary MINC tools from source. I don't recommend this option. >>> >>> 2) get the source and build locally. There is a special bundle of the >>> necessary MINC tools source code w/ build script that you can use to >>> build the tools on your own platform. Goto: >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ >>> >>> and read the file: mni.srcbuild.README.txt >>> then download the file: mni.srcbuild.tar.gz >>> and build locally. Give this a try only if the next option doesnt work. >>> >>> 3) download the binaries for centos4 that we've built and use locally. >>> they are found in: >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ >>> >>> and the file is called: mni-Linux-centos4-v1.4.tar.gz >>> >>> I just uploaded this, so you will be participating in an experiment of >>> sorts. To install, from the root directory /, type: >>> >>> tar zxvf mni-Linux-centos4-v1.4.tar.gz >>> >>> This will untar/unzip to /usr/pubsw/packages/mni/current which is where >>> we have the tools installed here at MGH. unfortunately, the MINC tools, >>> when built, hardcode installation paths into their workings, so if you >>> use this binary, you have to install in exactly this path. if you can't >>> then you will have to build from source. this is the can of worms that >>> i refer to.o. >>> >>> If you can untar/unzip the file to that directory, then you should not >>> see the error that you were seeing when you source SetUpFreeSurfer.csh. >>> If not seeing the error, then try typing this: >>> >>> nu_correct >>> >>> This is a minc tool, and if it runs correctly, will output this: >>> >>> nu_correct, version 1.10 >>> >>> Usage: nu_correct [-help] [options] in.mnc out.mnc >>> >>> If things are not installed, you will get some error about not finding >>> some perl related files. If so, your perl version may not match our >>> perl. Again, you will need to build from source in that case. >>> >>> Hopefully you can get the tools working, and please let me know how it >>> goes, as I have been deliberating for weeks now as to how to handle >>> this. In the past, we have let people fend for themselves or try to use >>> copies of our binaries, usually with limited success, so I would like a >>> better way to do things. >>> >>> Nick >>> >>> >>> >>> On Tue, 2005-08-23 at 17:30 -0400, Sasha Wolosin wrote: >>>> Hi Nick, >>>> I downloaded the distribution in FC4, put all the freesurfer files into a new folder (/freesurfer) and have adjusted the SetUpFreeSurfer.csh file accordingly for most of the directories, but I cannot find the MINC tools directory. So when I run the SetUpFreeSurfer.csh file, I get the following errors: >>>> >>>> WARNING: MINC_BIN_DIR not defined. >>>> 'nu_correct' and other MINC tools >>>> are used by some Freesurfer utilities. >>>> Set NO_MINC to suppress this warning. >>>> WARNING: MINC_LIB_DIR not defined. >>>> Some Freesurfer utilities rely on the >>>> MINC toolkit libraries. >>>> Set NO_MINC to suppress this warning. >>>> MINC_LIB_DIR: Undefined variable. >>>> >>>> Do you know if the MINC tools are included in this download? If not, where can I find them? >>>> >>>> Thanks, >>>> Sasha >>>> >>>> >>>> Sasha Wolosin >>>> Research Assistant >>>> Developmental Cognitive Neurology >>>> Kennedy Krieger Institute >>>> 707 N. Broadway >>>> Baltimore, MD 21205 >>>> ph: (443) 923-9270 >>>>>>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 08/23/05 11:58 AM >>> >>>> Sasha, >>>> >>>> I don't know if it will run on FC3. We do not test on that platform, >>>> just FC2 (and CentOS 4, and RH9). >>>> >>>> Nick >>>> >>>> On Tue, 2005-08-23 at 10:26 -0400, Sasha Wolosin wrote: >>>>> Hi Nick, >>>>> Do you know if this distribution will run on FC3? >>>>> 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. >>>>> >>>>> >>>> >>>> >>> >>> >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 jpacheco(a)nmr.mgh.harvard.edu

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Re: new Freesurfer version
by Sasha Wolosin 29 Aug '05

29 Aug '05

Here is the full command and output When I try to open the orig volume, I get the error: "First orig image: /freesurfer/subjects/2332/mri/orig/COR-001 not found" [root@localhost /freesurfer]# cd subjects/2332/mri/orig [root@localhost orig]# ls 2332_analyze 2332_crsg [root@localhost orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz reading from 2332_crsg/001... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image... ------------------------------------------------- DICOM meta-header file name 2332_crsg/001 Date and time study date 20030630 study time 101639.0000 series time 104735.12 acquisition time 104735.12 Identification patient name ... manufacturer Philips Medical Systems Dimensions number of rows 256 number of columns 256 number of frames 124 pixel width 0.9375 pixel height 0.9375 slice thickness 1.5 field of view 240 image number 1 (might be not reliable) Acquisition parameters echo time 6.00003 repetition time 35 inversion time not found echo number 1 flip angle 0.785398 bits allocated 16 Spatial information first image position -114.756 -101.936 133.356 last image position -126.115 82.1994 135.698 image orientation 0.998088 0.0614863 0.00638348 0.00559035 0.0130627 -0.999899 ------------------------------------------------- TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to 001.mgz... [root@localhost orig]# csurf Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 08/29/05 4:50 PM >>> p.s. in general please include the full command line and output, otherwise it's really hard to help you. Also, if you send these things to the freesurfer list your response time will get a lot better as there are a bunch of people who answer questions on it On Mon, 29 Aug 2005, Sasha Wolosin wrote: > Hi Nick, > > We now have the libraries installed, and we have managed to get freesurfer running on FC4, and I am able to convert from dicom to COR by typing: > mri_convert -it dicom -ot cor 2332_crsg/001 001 > > but I am having trouble converting to/ opening files in mgz format. When I specify the output type as mgz instead of cor, I get a "segmentation fault" and when I try to open the orig volume in csurf I get the error: > "First orig image: > /freesurfer/subjects/2332/mri/orig/COR-001 not found" > > Is this version of freesurfer not set up to use mgz files yet? Or is there some setting I must change? > > Thanks, > Sasha > > > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 >>>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 08/24/05 4:15 PM >>> > Sasha, > > Hi, Freesurfer requires the following libraries, which are sometimes > (and sometimes not) included in Linux distributions: > > tcl, tk, tix, blt, gsl, tiff, jpeg, and glut > > Usually, a sysadmin will install these, but we are finding that a lot of > people do not have the tcl/tk/tix/blt tools installed and working (and > that work well with freesurfer). > > So for now, you will need to install the tcl/tk/tix/blt tools. Or you > can try downloading a source code bundle, called fs_supportlibs.tar.gz > from our distribution site: > > http://www.bic.mni.mcgill.ca/software/distribution/ > > to untar/unzip, type: > > tar zxvf fs_supportlibs.tar.gz > > then type > > cd fs_supportlibs > setenv LIBS_DIR /usr > > then to build tcl and tk: > > ./build-tcltk.csh > > and tix and blt: > > ./build-tix.csh > ./build-blt > > Upon completion, you should see the libs in the /usr/lib directory. > I can't guarantee this will work well for you, some build engineer > skills are required if problems are encountered. You may want to have > your sysadmin do it. > > We are considering including some of these libs in the next release. > > As for not finding the nu_correct command, this seems to be more basic > problem. Are the installed MINC tools in your path? type: > > echo $PATH > > and look for /usr/pubsw/packages/mni/current/bin > > the SetUpFreeSurfer.csh script sets this up. > > Nick > > > On Wed, 2005-08-24 at 10:51 -0400, Sasha Wolosin wrote: >> Hi Nick, >> Thanks for the quick response. I downloaded the binaries from the distribution site (mni-Linux-centos4-v1.4.tar.gz) and I untarred the files to the /usr folder on my hard drive. I no longer get an error from the set up file, but freesurfer doesn't seem to be working properly. I am working with FC4, which we have recently installed and have not used yet, so I don't know if this could be a problem with our FC4 installation. Here's what I get when I run the set up and type some commands: >> >> [root@localhost /freesurfer]# tcsh >> [root@localhost /freesurfer]# source MySetUpFreeSurfer.csh >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /freesurfer >> FSFAST_HOME /freesurfer/fsfast >> SUBJECTS_DIR /freesurfer/subjects >> FUNCTIONALS_DIR /freesurfer/sessions >> MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin >> MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib >> PERL5LIB /usr/pubsw/packages/mni/current/lib/perl5/5.8.5 >> QTDIR /usr/lib/qt-3.3 >> [root@localhost /freesurfer]# csurf >> /freesurfer/bin//csurf: line 4: /usr/bin/tixwish: No such file or directory >> /freesurfer/bin//csurf: line 4: exec: /usr/bin/tixwish: cannot execute: No such file or directory >> [root@localhost /freesurfer]# nu_correct >> nu_correct: Command not found. >> [root@localhost /freesurfer]# tkmedit >> tkmedit: error while loading shared libraries: libtix8.1.8.4.so: cannot open shared object file: No such file or directory >> [root@localhost /freesurfer]# >> >> Thanks, >> Sasha >> >> >> Sasha Wolosin >> Research Assistant >> Developmental Cognitive Neurology >> Kennedy Krieger Institute >> 707 N. Broadway >> Baltimore, MD 21205 >> ph: (443) 923-9270 >>>>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 08/23/05 6:32 PM >>> >> Sasha, >> >> The MINC tools are not included in the freesurfer Linux download. >> These tools are a whole can of worms unto themselves, at least in >> terms of installation and integration with freesurfer, but there are >> three possibilities to get these tools: >> >> 1) get the binaries from the main MNI site: >> http://www.bic.mni.mcgill.ca/software/distribution/ >> >> you will need the NetCD, MINC and BICPL packages. I cannot say with >> certainty whether this will work with FreeSurfer, as we have built all >> the necessary MINC tools from source. I don't recommend this option. >> >> 2) get the source and build locally. There is a special bundle of the >> necessary MINC tools source code w/ build script that you can use to >> build the tools on your own platform. Goto: >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ >> >> and read the file: mni.srcbuild.README.txt >> then download the file: mni.srcbuild.tar.gz >> and build locally. Give this a try only if the next option doesnt work. >> >> 3) download the binaries for centos4 that we've built and use locally. >> they are found in: >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ >> >> and the file is called: mni-Linux-centos4-v1.4.tar.gz >> >> I just uploaded this, so you will be participating in an experiment of >> sorts. To install, from the root directory /, type: >> >> tar zxvf mni-Linux-centos4-v1.4.tar.gz >> >> This will untar/unzip to /usr/pubsw/packages/mni/current which is where >> we have the tools installed here at MGH. unfortunately, the MINC tools, >> when built, hardcode installation paths into their workings, so if you >> use this binary, you have to install in exactly this path. if you can't >> then you will have to build from source. this is the can of worms that >> i refer to.o. >> >> If you can untar/unzip the file to that directory, then you should not >> see the error that you were seeing when you source SetUpFreeSurfer.csh. >> If not seeing the error, then try typing this: >> >> nu_correct >> >> This is a minc tool, and if it runs correctly, will output this: >> >> nu_correct, version 1.10 >> >> Usage: nu_correct [-help] [options] in.mnc out.mnc >> >> If things are not installed, you will get some error about not finding >> some perl related files. If so, your perl version may not match our >> perl. Again, you will need to build from source in that case. >> >> Hopefully you can get the tools working, and please let me know how it >> goes, as I have been deliberating for weeks now as to how to handle >> this. In the past, we have let people fend for themselves or try to use >> copies of our binaries, usually with limited success, so I would like a >> better way to do things. >> >> Nick >> >> >> >> On Tue, 2005-08-23 at 17:30 -0400, Sasha Wolosin wrote: >>> Hi Nick, >>> I downloaded the distribution in FC4, put all the freesurfer files into a new folder (/freesurfer) and have adjusted the SetUpFreeSurfer.csh file accordingly for most of the directories, but I cannot find the MINC tools directory. So when I run the SetUpFreeSurfer.csh file, I get the following errors: >>> >>> WARNING: MINC_BIN_DIR not defined. >>> 'nu_correct' and other MINC tools >>> are used by some Freesurfer utilities. >>> Set NO_MINC to suppress this warning. >>> WARNING: MINC_LIB_DIR not defined. >>> Some Freesurfer utilities rely on the >>> MINC toolkit libraries. >>> Set NO_MINC to suppress this warning. >>> MINC_LIB_DIR: Undefined variable. >>> >>> Do you know if the MINC tools are included in this download? If not, where can I find them? >>> >>> Thanks, >>> Sasha >>> >>> >>> Sasha Wolosin >>> Research Assistant >>> Developmental Cognitive Neurology >>> Kennedy Krieger Institute >>> 707 N. Broadway >>> Baltimore, MD 21205 >>> ph: (443) 923-9270 >>>>>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 08/23/05 11:58 AM >>> >>> Sasha, >>> >>> I don't know if it will run on FC3. We do not test on that platform, >>> just FC2 (and CentOS 4, and RH9). >>> >>> Nick >>> >>> On Tue, 2005-08-23 at 10:26 -0400, Sasha Wolosin wrote: >>>> Hi Nick, >>>> Do you know if this distribution will run on FC3? >>>> 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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Freesurfer August 2005