Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

manual edit problem
by Kirk, Gregory 16 Jul '07

16 Jul '07

Hi, I am trying to fix the few subjects in my study ( 3 of 64 ) that need manual fixes resulting from skull strip erros ( 2 of 3 cerebelem was left out ). This is the first study since my student who was doing this for me left ... So the note he left said do tkmedit practice/subjectname/ brainmask.auto.mgz -aux orig.mgz then config brush, etc. i.e. make the edits and save changes in brainmask.auto.mgz with input from orig.mgz In the frresufer wiki tutorial it has tkmedit 091_watershed_before brainmask.mgz -aux T1.mgz i.e. make the edits and save changes brainmask.mgz with input from T1.mgz the study is with version freesurfer-v3.0 so the difference may be with version. I was unsure what to do after saving the edits, I tried copying brainmask.auto.mgz to brainmask.mgz, i.e. overwrote the file with cp. recon-all -autorecon2 -subjid <subject name> and it finished with errors. I could find no error message in the logs. I deleted the surfaces in the surface directory and reran and it again finished with errors and only 5 of the surfaces ( on the right side) had been produced. a bit mysterious since the left and right side was involved in the edits ?? anyhow see an obvious change in procedure I need to make ? thanks again Greg.

1 0

Mean cortical thickness as nuisance variable
by Juergen Haenggi 16 Jul '07

16 Jul '07

Dear Freesurfer users We are doing an analysis on cortical thickness and we are not sure whether to include the mean cortical thickness as a covariate of no interest in our statistical model. Any suggestions are welcome. Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

2 1

add the gray matter
by Wang, Xin 13 Jul '07

13 Jul '07

Hello, Group I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface? Thank you in advance. Xin

3 5

differences between mri_glmfit and intergroupavg-sess
by Robert Levy 13 Jul '07

13 Jul '07

Hello, I've comparing results of output from intergroupavg-sess with output from mri_glmfit, and the difference seems to be too huge to be accountable just from differences between the two programs. I attached images that go along with the commands below. What do you think could be the cause of these huge differences? Are there any parameters that might reduce the difference? Thanks, Rob (September 2005) intergroupavg-sess \ -group1 BwGroupNormalsError5 \ -group2 BwGroupAspError5 \ -space sph \ -spacedir sph_sm20 \ -intergroup BwGroupError5 \ -analysis EMerror \ -contrast ASevASc (Currently ran this because so I could then adjust the threshold using monte carlo data. The results of this should I think be the same or similar to the intergroupavg results) /space/greve/1/users/greve/freesurfer/bin/mri_glmfit \ --really-use-average7 \ --y rh.ASevASc_8s_BwGroupError5.fsfast.mgh \ --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd \ --glmdir rh.ASevASc_8s_BwGroupError5.fsfast.glmdir \ --pca \ --surf average7 rh \ --C fsgd_and_contrast_files/BwGroupError5.mat \ --label average7/label/dACC_rACC_final-rh.label \ --fwhm 4.6 -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

2 4

Conversion to Minc Line OBJ
by jorge luis 13 Jul '07

13 Jul '07

Hello all I would like to convert a freesurfer triangular surface (ASCII or binary) to Minc Line OBJ file format. I know how to convert to Minc Polygons OBJ file format, but it is not useful for my application. I need a conversion to the Lines OBJ format. Any help is welcome In advance thank you very much Jorge ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

2 1

control points
by Don Hagler 13 Jul '07

13 Jul '07

In recon-all, it says you are supposed to use -autorecon2-cp if you use control points. So I wonder why earlier normalization steps also use control points, such as Norm1 and CANormalize. What effect do the control points have in those steps? _________________________________________________________________ http://newlivehotmail.com

3 4

Problems with surfaces
by Alexander Fornito 12 Jul '07

12 Jul '07

Hi all, I'm trying to run some 3T data through freesurfer and encouter a consistent problem in the cuneus/occiptal lobes where the pial surface fails to extend the the grey/CSF boundary and instead follows the white surface. I have attached an example. This problem happens in the same area across a substantial proportion of my images. I've tried control points, but they don't seem to help. Any suggestions would be greatly appreciated. Thanks, Alex

2 1

Image scaling in the MGZ file format
by Jerry Yeou-Wei Chen 12 Jul '07

12 Jul '07

Hello Freesurfer Forum, We have a question about the M matrix, found in the .mgz file header. We loaded an .mgz file into Matlab and took a look at the affine transform matrix M from the header: M(1,:) = [-1 0 0 132.7486]; M(2,:) = [ 0 0 1 -105.7281]; M(3,:) = [ 0 -1 0 131.7424]; M(4,:) = [ 0 0 0 1 ]; Let's call these numbers: M(1,:) = [ a 0 0 xt ]; M(2,:) = [ 0 0 c yt ]; M(3,:) = [ 0 b 0 zt ]; M(4,:) = [ 0 0 0 1 ]; We interpret a b and c as controlling rotation. xt yt zt govern translation. However, we cannot see how this matrix controls scaling. We were expecting to see the following: M(1,:) = [ xs 0 0 xt ]; M(2,:) = [ 0 ys 0 yt ]; M(3,:) = [ 0 0 zs zt ]; M(4,:) = [ 0 0 0 1 ]; ...where xs yx zs control scaling. In our empirical matrix they do not seem to be serving that function. (xs appears to be used for rotation only, ys and zs are zero). So the first question is: does the matrix control scaling, and if so, how? The second question: Is the scaling built into the image, such that each voxel is 1mm by 1mm by 1mm? If so, how can the program tell when this is the case, and when it is not? Does ndim1 represent the number of voxels in that dimension, or the distance across that dimension in millimeters? Does ras_good_flag simply indicate that the image is in the proper orientation, or does it also indicate that each voxel in the image measures 1mm x 1mm x 1mm? Thanks for your help. Jerry Chen and Geoff Pope

3 2

few oasis question
by Martin Kavec 12 Jul '07

12 Jul '07

Hi. I have few questions regarding the recently published OASIS data analyzed using Freesurfer: 1. How did you produce $SUBJECT_ID/mri/wmparc.mgz. I am running recon-all -all on my subjects, but I don't get this file. 2. How did you produce segmentation of the corpus callosum. I am running recon-all -all on my subjects, but I don't get this file. 3. Why do the structure volumes differ between $SUBJECT_ID/stats/wmparc.stat and $SUBJECT_ID/stats/aseg.stat Thanks, Martin

3 6

flip functional using tkregister2?
by Stacy Chu 12 Jul '07

12 Jul '07

Hi all, I used reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 and then reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 --manual to register and edit the registration of a functional to its anatomical volume. The initial registration came out pretty bad and I think I need to do a left-right flip. I see that I can rotate/translate/resize using tkregister2, but I can't figure out how to make a flip. Does anyone know the best way to do that? If the registration looks so bad do I need to change something in the command for my initial registration process? Thanks! Best, Stacy ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

2 7

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer