Freesurfer October 2004

freesurfer@nmr.mgh.harvard.edu

27 participants
37 discussions

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

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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

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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

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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

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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

Update mri_convert and mri_parse_sdcmdir
by Kevin Teich 13 Oct '04

13 Oct '04

Thanks to Keith Schneider, we discovered memory related problems when reading Siemens DICOM files. This update should fix those bugs. There are two programs, mri_convert and mri_parse_sdcmdir, and they should go into your $FREESURFER_HOME/bin/$OS directory. Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_convert-20041012-Darwin.tar.gz Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_convert-20041012-Linux.tar.gz -- Kevin Teich

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could you please tell me how to use mris_anatomical_stats?
by Wan Park 12 Oct '04

12 Oct '04

or where I can read more about it? Thanks, Wan

3 2

Processing woes
by Kai Schreiber 08 Oct '04

08 Oct '04

Hi there, I just installed freesurfer, and I apologize if I'm missing something simple. We read in structural data in AFNI's BRIK and HEAD format. Everything works fine, until we run the white matter fill. This will write about 20K/second of error messages to error.log and run for several hours, only to complete without creating usable output. We then of course get an error message for Tesselation complaining about the previous step's lack of output. The error.log file contains just a gazillion copies of this single line (recently it ran up to almost 1GB of it) MRIvoxelToTalairachVoxel: unsupported slice direction -1 What gives? Cheers, Kai -- Kai Schreiber PhD, School of Optometry, UC Berkeley 360 Minor Hall, Berkeley, CA 94720-2020, USA Phone ++1 510 642 7710 http://genista.de/kai/kschreiber.html

2 1

displaying annotation
by Keyma Prince 08 Oct '04

08 Oct '04

Hello, I would like to import the annotation file into the csurf but with only certain labels produced by parcellate subject. I would like to use this to display some of the labels produced by the parcellate subject onto the inflated brain. Do I have to extract the labels from the annotation file first? -Keyma Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

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Freesurfer October 2004