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@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@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@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@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:
- 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.
- 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.
- 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@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
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