Freesurfer

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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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fsl_rigid_register
by Steve Stufflebeam 29 Aug '05

29 Aug '05

fsl_rigid_register is not as it has in the past. It seems the script isn't writing the correct outvol.* format in the /tmp directory. My command line and output are below. Thanks, --Steve lucy [flash] fsl_rigid_register -r orig.mgh -i flash5.mgh -o flash5_fsl.mgh $Id: fsl_rigid_register,v 1.7 2003/08/21 23:28:03 ebeth Exp $ Mon Aug 29 09:31:13 EDT 2005 flash5_fsl.mgh -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash mri_convert orig.mgh /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img mri_convert orig.mgh /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img reading from orig.mgh... TR=2000.00, TE=3.37, TI=950.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img... Analyze Output Matrix -1.000 -0.000 -0.000 129.806; -0.000 0.000 1.000 -58.312; 0.000 -1.000 -0.000 126.746; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to 'coronal flipped' -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash mri_convert flash5.mgh /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.imgmri_convert flash5.mgh /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.img reading from flash5.mgh... TR=20.00, TE=1.80, TI=1.80, flip angle=5.00 i_ras = (0.0729938, -0.963132, 0.258938) j_ras = (0.0105586, -0.25887, -0.965855) k_ras = (-0.997276, -0.0732354, 0.00872654) writing to /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.img... Analyze Output Matrix 0.073 0.011 -1.326 76.077; -0.963 -0.259 -0.097 234.646; 0.259 -0.966 0.012 88.186; 0.000 0.000 0.000 1.000; -------------------- No such orientation specified in Analyze7.5. Set orient to 0 Direction cosines for /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash/flash5.mgh are: x_r = 0.0730, y_r = 0.0106, z_r = -0.9973, c_r = 0.6410 x_a = -0.9631, y_a = -0.2589, z_a = -0.0732, c_a = 70.6763 x_s = 0.2589, y_s = -0.9659, z_s = 0.0087, c_s = -2.2521 INFO: set hdr.hist.orient to 'transverse unflipped' -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash tkregister2 --targ orig.mgh --mov flash5.mgh --reg /tmp/fsl_rigid_register.6917/tkregister.dat --fslregout /tmp/fsl_rigid_register.6917/initxfm.fslmat --regheader --noedit --s doesnotmatter target volume orig.mgh movable volume flash5.mgh reg file /tmp/fsl_rigid_register.6917/tkregister.dat LoadVol 0 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 INFO: loading target orig.mgh 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 flash5.mgh Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.330 -85.120; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 ---- Input registration matrix (computed) -------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; subject = doesnotmatter RegMat --------------------------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; register: file /tmp/fsl_rigid_register.6917/tkregister.dat written Init FSL Mat based on geometry ------------------- -0.07299379 -0.01055863 0.99727648 53.97108841 -0.25893784 0.96585459 -0.00872653 38.25601959 -0.96313190 -0.25886959 -0.07323541 290.63790894 0.00000000 0.00000000 0.00000000 1.00000000 ------------------------------------------------- -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash flirt -in /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.hdr -out /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.hdr -init /tmp/fsl_rigid_register.6917/initxfm.fslmat -omat /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash mri_convert /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img flash5_fsl.mgh mri_convert /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img flash5_fsl.mgh reading from /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img... ERROR: analyzeRead(): cannot find any files for /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img

3 2

encounter error during fill
by Yuan-Fen Kuo 29 Aug '05

29 Aug '05

Hi. I am ( again) trying out the stage1 work flow. I have been encountering the following error during the fill step which terminates the work flow. mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status recon-all exited with errors at Mon Aug 29 14:02:23 CDT 2005 how may I go about solving this? The complete output is at the end of the message. Thank you for help, Eric Yuan-Fen Kuo Associate Imaging Processing Specialist Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison --------------------------------------------- Fill Mon Aug 29 14:01:26 CDT 2005 INFO: Uses mri/transforms/talairach.xfm mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm wm filled /Users/Shared/freesurfer/subjects/005CO/mri logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Volume /tmp/mritotal_20452/nu_8_dxyz.mnc cannot be found. INFO: Using transforms/talairach.xfm and its offset for Talairach volume ... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.078 -0.013 -0.035 -5.822; 0.018 1.076 0.141 -29.222; 0.032 -0.136 1.035 16.018; 0.000 0.000 0.000 1.000; mri_fill: could not find valid seed for the cc No such file or directory Looking for area (min, max) = (350, 1400) area[0] = 12102 (min = 350, max = 1400), aspect = 0.79 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... Looking for area (min, max) = (350, 1400) area[0] = 12102 (min = 350, max = 1400), aspect = 0.79 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status recon-all exited with errors at Mon Aug 29 14:02:23 CDT 2005

2 1

Cannonical Registration
by Yuan-Fen Kuo 26 Aug '05

26 Aug '05

Hi: I am trying out the recon-all command with the -stage1 workflow. The Cannonical Registration ( mri_ca_register) runs for many many hours. I have not found much reference regarding this step. It is not mentioned in the help in the -stage1 section, nor is it mentioned under step-wise directives. Is this a necessary step if I'd just like to have basic segmentation and being able to proceed to the manual editing procedure? Thank you, Yuan-Fen Kuo Associate Imaging Processing Specialist Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison

2 1

Distributions: which? ; Archives -- forbidden
by Graham Wideman 26 Aug '05

26 Aug '05

Folks: I would like to get up-to-date on our FreeSurfer installation. Are there some notes which describe the various snapshots at: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ ? In particular, some of these downloads are much huger than others, which makes one wonder what's included in each. I also tried to see if there were some email messages covering this in the archives, but the archive seems to be broken currently: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/ ... returns "Forbidden" -- ie: permissions problem. Regards, Graham

2 1

parcellation of frontal lobe
by marc ruiz 26 Aug '05

26 Aug '05

2 1

autorecon1 difficulty
by Elizabeth Fenstermacher 25 Aug '05

25 Aug '05

Hello, I was trying to test the autorecon tools that we're planning to use to process some of our newer data. In order to do so I sourced source /usr/local/freesurfer/nmr-dev-env Then after setting my subject directory [/space/thigpen/1/users/efenster/example] typed: recon-all -subjid 002 -autorecon1 It failed during the intensity normalization I believe yielding the following error message ----------------------------------------------------------------------------------- BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. ERROR: nu_correct recon-all exited with errors at Thu Aug 25 14:23:21 EDT 2005 ----------------------------------------------------------------------------------- When viewing the file it sites as being problematic it seems to be the initialization of one of the MNI tools, specifically the following line use MNI::Startup qw(nocputimes); Is there a problem in how I initialized FreeSurfer that created this error and if so how would it be recommended to initialize FreeSurfer in order to use the autorecon tools? Thank You Eliz

2 2

ERROR:nu_correct
by Margaret Duff 25 Aug '05

25 Aug '05

Hello, I am running the command: recon-all -subjid SM2S12_autoreconall -autorecon1 -notalairach on troy and getting the following error message: --------------------------------------------- Nu Intensity Correction Thu Aug 25 12:11:42 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, -1.01845e-10, -1.20596e-09) j_ras = (-1.65567e-09, 6.42749e-09, -1) k_ras = (-2.65927e-10, 1, 9.43205e-09) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mduff@troy:/autofs/space/troy_001/users/FREESURFER/SM2S12_autoreconall/mri/] [2005-08-25 12:11:52] running: /usr/pubsw/packages/mni/current/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 /usr/tmp/nu_correct_27529/ nu0.mnc nu1.imp /usr/pubsw/packages/mni/current/bin/volume_stats: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct recon-all exited with errors at Thu Aug 25 12:11:53 EDT 2005 This command was working yesterday, so I am not sure what has changed over night. Thanks for your help, Margaret

2 3

COR to BRIK
by Michele Perry 25 Aug '05

25 Aug '05

Hi, Is there a way to view an aseg with colors in afni once it has been converted to .img? Michele

2 1

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