Freesurfer September 2004

freesurfer@nmr.mgh.harvard.edu

19 participants
20 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

4 3

problem to source FreeSurfer.cshrc
by Sepideh Sadaghiani 29 Sep '04

29 Sep '04

Hello, I'm trying to install FreeSurfer0.8 on linux. Since the linux computer doesn't have an internet connection, I write off what from the shell: [sepirat@localhost sepirat]$ ls etc/ FreeSurfer.cshrc [sepirat@localhost sepirat]$tcsh : Command not found. : Command not found. : label not found. [sepirat@localhost ~]$ source etc/FreeSurfer.cshrc : Command not found. : Command not found. : label not found. [sepirat@localhost ~]$ newdefs newdefs: Command not found. I don't have a solid unix background. Is this a problem with tcsh? Sep -- +++ GMX DSL Premiumtarife 3 Monate gratis* + WLAN-Router 0,- EUR* +++ Clevere DSL-Nutzer wechseln jetzt zu GMX: http://www.gmx.net/de/go/dsl

3 2

tkmedit question
by George Papadimitriou 29 Sep '04

29 Sep '04

Hi all, How can I compute the volume of a label created using tkmedit? Is there a program to do this, or is it sufficient to count the number of points listed in the label file and multiply by the volume per voxel? (And if so, is the volume per voxel the voxel size for my original 40 slice axial volume, or the voxel size for the 256 slice resampled volume that tkmedit displays?) Thanks, George P.

4 4

MacOSX mri_convert probelm fixed
by Yasunari Tosa 20 Sep '04

20 Sep '04

Hi, MacOSX people: We discovered a major problem in mri_convert for MacOSX. The problem ========= mri_convert COR file into mnc format produces the wrong byte order and thus "mincinfo" on that file does not work. The new binary =========== The file was compiled under Panther 10.3.5 (Darwin 7.5.0) and optimized for G4 (new trend). (Note that otool reveals the dependency in two fink libraries /sw/lib/libjpeg.62.dylib, /sw/lib/libtiff.3.dylib, and two system libraries: /usr/lib/libz.1.dylib, /usr/lib/libSystem.B.dylib). The check with minc compatibility ========================= I downloaded the latest MNI MacOSX binaries from http://www.bic.mni.mcgill.ca/software/distribution/#osx installed in /usr/local/mni. The comments =========== 1. If you need Jaguar version 10.2.x, please let me know. 2. If it won't run on your powerful G5, I will try to find G5 to compile. How-to-get-it ========== ftp surfer.nmr.mgh.harvard.edu use anonymous and passwd as your email address > cd pub/dist > get mri_convert-040920-Darwin.gz Thank you. Tosa Yasunari Tosa, Ph.D. Email: tosa(a)nmr.mgh.harvard.edu NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street Charlestown, MA 02129 USA

1 0

questions on mkbrainmask-sess
by Jia Liu 20 Sep '04

20 Sep '04

Dear all- Today I tried mkbrainmask-sess (first time), and got the error message shown below: +++++++++++++++++++++++++++++++++ zion:/nfs/home/jliu/VM/myProc> mkbrainmask-sess -sf sessid_S001 -df sesspar -funcstem fmcss ------------------------------------------------ ------------------------------------------------ /nfs/home/jliu/VM/S001 Mon Sep 20 21:20:40 CST 2004 -------------------------------------------------- /nfs/home/jliu/VM/S001/bold mkbrainmask -i 004/fmcss -o masks/brain -thresh 0.1 -umask 2 -------------------------------------------------- Scratch Dir is /tmp/mkbrainmask_23685 # ---------- Converting bvolume to .img ------------------ # mri_convert 004/fmcss_000.bshort /tmp/mkbrainmask_23685/fmcss.img reading from 004/fmcss_000.bshort... INFO: bvolumeRead: min = 25, max = 1325 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.995227, 0.0975827) k_ras = (-0, 0.097583, 0.995227) writing to /tmp/mkbrainmask_23685/fmcss.img... Analyze Output Matrix -1.406 0.000 -0.000 94.016; 0.000 -1.400 0.195 101.727; 0.000 0.137 1.990 -42.636; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to 3 # ---------- Using FSL's BET to Extract Brain------------------ # This program has not been compiled for this data type /nfs/home/jliu/VM/S001/bold bet /tmp/mkbrainmask_23685/fmcss /tmp/mkbrainmask_23685/brain -m -f 0.1 ERROR: bet failed ERROR: mkbrainmask failed Exit 1 +++++++++++++++++++++++++++++end+++++++++++++++++++++++++ The input data (fmcss) were motion-corrected, spatial-smoothed, and intensity-normalized using fsfast (the newest version released). Could anyone tell me how to fix this problem? Thanks for your help! jia

1 0

mincinfo error opening "orig.mnc"
by Mithun Mukherjee 17 Sep '04

17 Sep '04

Hi everybody, I am trying to run segment_subject on one run of data which was originally in BRIK format and then converted to COR using mri_convert. In the initial registration to talairach process, mincinfo can't seem to read the .mnc file that mri_convert gave it. As a result the talairach.xfm transformation matrix is not created by mritotal. The remaining procedures continue but I'm not sure if the registration to talairach space worked. I checked the file permissions on orig.mnc and that doesn't seem to be the problem. Is the COR to .mnc conversion the source of the error ? I tried reading the image information from "orig.mnc" independently with mincinfo but that didn't work either. Below are the error logs for both mincinfo and segment_subject. Thanks for your help. Mithun -- Rochester Center for Brain Imaging University of Rochester Medical Center 575 Elmwood Avenue, Annex Room 1B-101 Rochester, NY 14642 Ph: 585-275-4585 [pyramidal:aparna/mri/orig] madmin% mincinfo -image_info orig.mnc ncopen: filename "orig.mnc": Invalid dimension id or name miopen: MINC package entry point [pyramidal:aparna/mri/orig] madmin% [pyramidal:/usr/local/freesurfer] root# segment_subject aparna cp: /usr/local/freesurfer/subjects/scripts/brain.dat: No such file or directory /usr/local/freesurfer/subjects/aparna/scripts /usr/local/freesurfer registering aparna mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: Error opening file "orig/orig.mnc" Error executing mincinfo on orig/orig.mnc Error: could not open file "/usr/local/freesurfer/subjects/aparna/mri/transforms/talairach.xfm". System message: No such file or directory mri_add_xform_to_header: could not read xform file '/usr/local/freesurfer/subjects/aparna/mri/transforms/talairach.xfm' No such file or directory reading from ../mri/orig... normalizing image... MRInormInit: Talairach origin at (128, 147, 114) wsize 10, windows 14 above, 9 below max gradient 1.000 0: 82 --> 82 1: 87 --> 113 2: 92 --> 119 3: 97 --> 121 ........ ........ .........

3 3

bad segmentation [newbie]
by F.Musso 17 Sep '04

17 Sep '04

Hi to all, In our last analysis, among 12 subjects after "-stage 1" and "-stage 2" we got only 3 reasonable brain surfaces. Most of the other brains have a very odd shape: -pieces of skull -coharse lack of cortex -holes -bridges -bad cutting planes -cerebellar attachments It seems to be a segmentation problem. How to solve some of these problems is clearly explained in the 'FreesurferGuide' but the whole analysis seems to be "too much affected"! I have to fix those errors manually? Can repeat the -stage 1 changing some parameters in the intensity normalization and/or segmentation process? I attach some examples (small jpg files) Thank you in advance. Cheers Francesco Musso Laboratory of Molecular Neuroimaging & Electrophysiology, Department of Psychiatry, Johannes Gutenberg-University, Mainz, Germany

2 2

Update for mris_register
by Kevin Teich 16 Sep '04

16 Sep '04

There is an updated version of mris_register available for download. Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Darwin.tar… Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Linux.tar.… Download the tarfile and expand it in your FREESURFER_HOME/bin/OS/ directory. -- Kevin Teich

2 1

mris_reverse
by Rutvik Desai 15 Sep '04

15 Sep '04

We need to L-R flip our surface data. I found a mention of mris_reverse in the mail archive and it appears that this program can do this, but it is not in the distribution we have. Is there a way to get it? There is no need for the flipped surfaces to be aligned to the volume; we just need the surfaces to look like they are from the other side. thanks, Rutvik

1 0

Fw: Freesurfer new release
by F.Musso 15 Sep '04

15 Sep '04

Hi to all, On the Freesurfer homepage I notice that via 'ftp' it's avaliable a new version of Freesurfer x Linux (26.08.2004). But there's nothing about it neither on the mail list nor on the homepage... It's just a 'beta' version? Cheers Francesco Musso MD Laboratory of Molecular Neuroimaging & Electrophysiology, Department of Psychiatry, Johannes Gutenberg-University, Mainz, Germany

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer September 2004