Freesurfer May 2009

freesurfer@nmr.mgh.harvard.edu

81 participants
126 discussions

Problem with space in directory or file name
by Ed Gronenschild 06 May '09

06 May '09

Hi, Whenever I want to convert DICOM files to .mgz file I have to remove spaces in the directory name or file names otherwise recon-all -i ... -s ... will not work. Bracketing the names within quotes will not help. Is there some workaround? ed

2 1

problem downloading freesurfer
by Dana W. Moore 05 May '09

05 May '09

I am trying to download FreeSurfer onto a different Linux machine. I am able to download, but when I try to unzip the files, I get this error message: gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now I have tried downloading it repeatedly with the same outcome. Do you know what the problem might be? I am downloading the <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.3.0/freesurfer-Linux…>freesurfer-Linux-centos4-stable-pub-v4.3.0-full.tar.gz file. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

2 3

fMRI FOV issue (Bay 8)
by Dave Brohawn 05 May '09

05 May '09

Hello, My bugr info is at the bottom, if needed: I was doing a recon-all on one of our subjects, and I received this error message: **************************************** ERROR! FOV=320.000 > 256 Include the flag -cw256 with recon-all! **************************************** I pasted this error message into the archives, and saw Nick had asked someone with a similar problem to check the FOV of their subject to see if it was greater than 256 via mri_info orig.mgz. Our subject, FB0011055B, has an FOV of 320, and dimensions 320 X 320 X 320. This is unusual because we opened the same set protocol as we usually do and did not make any adjustments to the FOV or slice parameters. Most of our subject's orig.mgz info looks like this - Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2200.00 msec, TE: 1.54 msec, TI: 1100.00 msec, flip angle: 7.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -0.7146 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 24.6542 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -26.7758 talairach xfm : /autofs/space/seymour_001/users/folate_subjects/FB0011053B/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 127.2854 0.0000 0.0000 1.0000 -103.3458 0.0000 -1.0000 0.0000 101.2242 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 127.2854 -0.0000 -0.0000 -1.0000 101.2242 -0.0000 1.0000 -0.0000 103.3458 0.0000 0.0000 0.0000 1.0000 This subject's is different, and it looks like this: Volume information for orig.mgz type: MGH dimensions: 320 x 320 x 320 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 320.000 dof: 0 xstart: -160.0, xend: 160.0 ystart: -160.0, yend: 160.0 zstart: -160.0, zend: 160.0 TR: 2200.00 msec, TE: 1.54 msec, TI: 1100.00 msec, flip angle: 7.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.2500 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 158.7500 0.0000 0.0000 1.0000 -160.0000 0.0000 -1.0000 0.0000 160.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 158.7500 -0.0000 -0.0000 -1.0000 160.0000 -0.0000 1.0000 -0.0000 160.0000 0.0000 0.0000 0.0000 1.0000 Any ideas as to why this would happen? Also, what does this -cw256 flag do and will it fix the issue? **************************************** ERROR! FOV=320.000 > 256 Include the flag -cw256 with recon-all! **************************************** Thank you, Dave Brohawn FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090503 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/1/users/folate_subjects PWD: /space/seymour/1/users/folate_subjects ssh seymour setenv SUBJECTS_DIR /space/seymour/1/users/folate_subjects cd /space/seymour/1/users/folate_subjects

2 1

mris_preproc really averages?
by Jeff Sadino 04 May '09

04 May '09

Hello, I ran mris_preproc on 56 subjects and then graphed the concatenated image. I also read this image into matlab and did the averaging using matlab, and then graphed the resulting image. When I did this, the two average pictures were slightly different. I thought that mris_preproc just simply averages all the subjects into common space. I noticed that its vector in matlab keeps the thickness value for all vertex's for all 56 subjects. I want to have the matlab capability for some custom processing I am doing, but the discrepancy leads me to think that mris_preproc is not a simple average. Can anyone elucidate this for me? Thank you! Matlab script. Only place I would suspect a wrong assumption is when I throw out the rest of the subjects at curv4=curv3(1,:,:,1) %Select your input thickness file path='/mnt/users/Jeff/fs/lc/HIV/pass2pics/416/diff/nc.rh.ave.mgh'; %Read the thickness file curv=MRIread(path); %Select the volume attribute curv2=curv.vol; %Create a duplicate thickness array for manipulation curv3=curv2; %Get the number of concatanated subjects tmp=size(curv2); m=tmp(4) clear 'tmp' %Sum each vertex for all your subjects for im=2:m for in=1:7 curv3(1,:,in,1)=curv3(1,:,in,1)+curv2(1,:,in,im); end end %Select just the first frame curv4=curv3(1,:,:,1); %Compute the average thickness curv.vol=curv4/m; %Write to thickness file MRIwrite(curv,'nc.rh.ave1.tmp.mgh'); _________________________________________________________________ Rediscover Hotmail®: Get quick friend updates right in your inbox. http://windowslive.com/RediscoverHotmail?ocid=TXT_TAGLM_WL_HM_Rediscover_Up…

4 3

Analysis without and with a covariate
by Jürgen Hänggi 04 May '09

04 May '09

Dear FS experts I have done an analysis without a covariate. Now, I want to do the same analysis but including mean cortical thickness as a covariate. I am wondering whether I have to run all steps again incl. mris_preproc or whether it is sufficient to only run mri_glmfit with the new FSGD file that includes the covariate. Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 1

recon-all w/ custom aseg atlas.
by Jamie Hanson 04 May '09

04 May '09

Hi Freesurfer folks- So I have been trying to create a custom aseg atlas (which I did, thanks much to Bruce and Nick!)... Now I want to run recon-all w/ that new custom aseg atlas (on additional subjects not included in .gca / atlas creation)... I checked the web and the listserv archive, but might have missed it... Is there an easy way to simple specify this new aseg atlas to run w/ recon-all? Or do I just need to run each command for autorecon1 and autorecon2 and just replace the default .gca file when I run mri_em_register, mri_watershed, mri_ca_normalize, mri_ca_register, mri_remove_neck, and mri_ca_label? Thanks much! jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/

2 1

letters of support
by Bruce Fischl 04 May '09

04 May '09

Hi All, we are planning on putting in a grant for software development to include automated tractography into FreeSurfer. The end result we envision will be a procedure much like recon-all, but applied to diffusion data that will automatically generate models of a set of tracts such as fornix, CST, cingulum, optic radiation, etc.... One of the critical factors in reviewing these grants is the extent to which the proposed project will impact a large user community, so it would be a big help to us if anyone who might be interested in using such a tool were to send us a letter (on official letterhead) stating this. Ideally this would also include an estimate of the # of subjects you would study in the next 5 years, and a reference to any funding source that would be used for the study if the tools were developed and distributed. The grant needs to be completed in the next 10 days or so, so sooner is better than later for us :). thanks Bruce

1 0

display registered sphere in surface?
by Zhong Jidan 04 May '09

04 May '09

Hi, I have a question about the sphere registration. The registration of surface is spherical registation, so the outpput of the surface is also a sphere. When we have the inflated and smoothwm, we can convert the surface into sphere using mris_sphere, but reversely, how to convert the deformed sphere in the form of white surface or pial surface? Also, if I want to use the surface between the white and pial surface to do registration, do I need to make the sphere myself? Thanks, -- Regards, Jidan

2 1

04 May '09

Research position (PhD) in Cognitive and Developmental Neuroscience at the Dpt. of Child and Adolescent Psychiatry, RWTH University of Aachen/JARA-Brain Translational Brain Medicine The successful applicant will be conducting in research projects with a particular focus on the development of normal and disturbed cognitive and emotional processes using methods related to structural and functional magnetic resonance imaging, neuropsychological and neurochemical techniques. The position will be a 3-year position (Verg. Gr 0,5 TVL13) with the possibility of renewal after positive evaluation. A considerable amount of work will take place at the Jülich Research Centre, one of the world's leading research facilities. The position is funded by the Excellence Initiative of the German federal and state governments. In 2007, the RWTH Aachen earned the connotation of being an elite university in Germany. Profile of applicant: - University Diploma/Degree in Psychology, Medicine, Biology, Physics, Bioinformatics or other related fields of natural sciences. - Experience with MRI/fMRI - Current driver`s license. Candidates holding a Master's/University diploma/degree in the natural sciences or related disciplines and an excellent academic record may apply by 1 June 2009 or also independent of deadlines. Interested applicants should send their materials online (preferred) and also via post to: Prof. Dr. med. F.D. Zepf, Juniorprofessor for Translational Neuroscience in Psychiatry and Neurology Dpt. of Child and Adolescent Psychiatry and Psychotherapy RWTH University of Aachen Neuenhofer Weg 21 52076 Aachen Germany Phone: +49-(0)241-8085504 Fax: +49-(0)241-8082544 Email: fzepf(a)ukaachen.de

1 0

MRISunfold error
by Hsin-Hao Yu 04 May '09

04 May '09

Hi, I run "mris_flatten" and got this message: "reading patch ../subjects/shiva/surf/lh.occip.patch.3d with 6095 vertices (98.2% of total)removing ripped vertices and faces...removing ripped vertices and faces...reading original vertex positions...minimizing metric distortion induced by projection...MRISunfold: could not open log file lh.occip.patch.flat.out" It's probably a very simple matter of fixing the unix permission, but I have no idea where MRISunfold is trying to save to. I checked every directory under the subject and found nothing unusual. Does anyone know which directory *.flat.out goes to? Thanx. Hsin-Hao

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 May 2009