Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

(no subject)
by Joongnam Yang 19 Oct '04

19 Oct '04

Hi, I used the following command recon-all -stage1 -subjid blobby and I got the following error message (Please let me know what is wrong with Freesurfer). -------------- copy of the exact error messages ------------------- ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source//minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.8 2002/08/05 00:53:50 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 6.11 2002/11/06 13:32:23 jason Exp $ $Header: /software/source//minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.4 2001/04/24 13:38:42 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ strings: nu_correct:: No such file or directory strings: Command: No such file or directory strings: not: No such file or directory strings: found.: No such file or directory $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is /home/nam ERROR: nu_correct does not exist --------- end of the copy of the error messages --------------------------

2 1

mri_montion_correct2 utility
by Kushal Koolwal 19 Oct '04

19 Oct '04

hi everyone, Well I couldn't run the mri_motion_correct on my Mac machine but I found another tool called mri_motion_convert2 in the /bin/noarch folder of freesurfer. I was able to run the utility by specifying output directory and the input files. But after it did all the processing it gives an error like: Motion Correcting /tmp/cor-2.mnc Mon Oct 18 15:03:59 PDT 2004 Error: opening MINC file "/tmp/cor-2.mnc". Error in minctracc in file minctracc.c, line 381 Cannot input volume '/tmp/cor-2.mnc'ERROR: mritoself failed [d99-94:bert/mri/orig] scottfre% I am attaching the error log file if any one wants to have a detail look. Sincerely, Kushal Koolwal _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com

5 5

mri_montion_correct command not found on Mac OS X
by Kushal Koolwal 19 Oct '04

19 Oct '04

hi, I am using MAC OS X and when i try to run the mri_motion_correct command it says that this command should be run on a linux machine. DoI have to use the register.csh command that they have specified in the manual. I even did that once but I got errors in between the process. this is the output that I get when I try to run mri_montion-convert. [d99-94:bert/mri/orig] scottfre% ls 001 002 003 [d99-94:bert/mri/orig] scottfre% mri_motion_correct . 001 002 003 mri_motion_correct must be run on a Linux machine thanks. Kushal _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com

3 3

Freesurfer download site
by Kristine Beate Walhovd 19 Oct '04

19 Oct '04

Hi I was just going to download Freesurfer again. However, the Freesurfer site I have used previously seem sto be down: http://surfer.nmr.mgh.harvard.edu Do I have the wrong address? I'd be grateful for directions on where to find the latest version now. Thanks, Kristine

1 0

cutting planes
by Daniel Wehner 18 Oct '04

18 Oct '04

Hi, Is there a good way to ensure that the cutting planes are accurate for segmenting the white matter? In some subjects, it appears that their head was tilted in the scanner, so some slices contain both RH and LH white matter. Because of this, the cerebellum sometimes gets connected during mri_fill and inflate_subject exits before the brain can be inflated. Here is the last few output lines when it exits: badRH = 23027/273213, badLH=41/234276 Please check filled volume. Cerebellum may be included. Thanks, Dan

2 1

working with *.mgh files
by Irina Sigalovsky 18 Oct '04

18 Oct '04

Hi, I was wondering if there is a way to invert *.mgh files (i.e., for each voxel, newvalue = 1/value). For example, is there a way to load *.mgh files into matlab? I need this to calculate R1 from T1.mgh. Thanks, Irina

2 1

Parcellation
by Calabrese, Massimiliano (NIH/NINDS) 18 Oct '04

18 Oct '04

Hello everybody I have the problem with Parcellation: Setenv CSURF_DIR subjectname ok Parcellate_subjectname error home/calabrem/freesurfer/subjects/01165> parcellate_subject 01165 reading atlas from 01165/average/lh.atlas2002_simple.gcs... GCSAread(01165/average/lh.atlas2002_simple.gcs): could not open file No such file or directory mris_ca_label: could not read classifier from 01165/average/lh.atlas2002_simple.gcs No such file or directory I need help :))) Could anyone help me? Thanks a lot Massimiliano

3 2

inflated surface not appearing
by Margaret Duff 18 Oct '04

18 Oct '04

Hi, I have run the process volume and create surface commands on a set of structural data, but when i go to edit segmentation, nothing comes up in the TkSurfer window. There are pictures in the TkEdit window, though. I have looked through my files and the surf folder has both lh and rh files in it so I was wondering if anyone had any idea why the inflated surface will not show up in TkSurfer. The only step I have omitted during processing is the Talairaching step. Thanks for your help, Margaret

1 0

mri_convert and COR files
by Kushal Koolwal 15 Oct '04

15 Oct '04

Hi, > I downloaded the raw data set for the subject called 'bert' and found 3 directories named 001 002 003 under it. And each of the directories contains files from COR-001 to COR-256. > Now the manual says to use mri_convert > ************************************************* > I. Data Conversion from the Unix/Linux Command Line > Conversion of native MR data to COR format is > performed using a process called mri_convert. > Enter the mri/orig directory in the Unix/Linux command > line. This is where the raw MR data files are > located. Type in the Unix/Linux command line: > mri_convert > <name_of_structural_run>/<first_MR_acquisition> > Where <name_of_structural_run> refers to the directory > of the structural run to be converted and > <first_MR_acquisition> refers to the first slice of > the structural run. For example: mri_convert > 002/I.001 Repeat this step for all the structural > runs that will be motion corrected and averaged for > reconstruction. > *************************************************************** > > Now my problem is how do I get the file name I.001 > which they have shown in the example. Also it says > that mri_convert command converts from native formats > to COR formats and I guess that the Raw Data files > downloaded already has the files in COR format. > > Basically I want to run the first 3 steps i.e convert, > motion correction and averagin as shown in the manual. > > Sincerely, > > Kushal _______________________________ Do you Yahoo!? Express yourself with Y! Messenger! Free. Download now. http://messenger.yahoo.com

3 2

spatial smoothing
by Irina Sigalovsky 13 Oct '04

13 Oct '04

Hi, I was wondering what exactly it means to smooth a surface with a step of 2 (i.e., what filter and parameters are used). Thanks, Irina

3 2

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Freesurfer