Freesurfer November 2006

freesurfer@nmr.mgh.harvard.edu

41 participants
59 discussions

aseg, aparc regions reference table (aka "data dictionary")?
by Graham Wideman 22 Dec '06

22 Dec '06

Folks: It would be *really* great if there was a page somewhere (or just a file) giving some info on the various measures that are captured in the aseg and aparc files. For each measure (in the table or the "comments" above the table): -- Description of what it includes -- some are obvious from the name, others not. -- Whether it's deprecated. -- Whether FS V-whatever actually produces this value, or just zero. (Very useful, and probably not too much work? Plus I'd like to adapt this info so as to pull only the non-inert rows from the data file). (Or is there some other way to determine this?) -- Some suggestions on what numbers need to be added to get popular subtotals. I've just read through the last six months of freesurfer list traffic, and I see numerous questions along these lines... and replies with some clues here and there. Also references to papers, but these don't detail the nitty gritty of what FS V-something actually does. Probably numerous users would get a lot of use out of having this info in one place. Thanks, Graham

2 1

new Intel Mac freesurfer distribution
by Nick Schmansky 04 Dec '06

04 Dec '06

Intel Mac owners, A distribution of Freesurfer is now available for the new Intel- processor Macs. It can be downloaded here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ Look for the file: freesurfer-Darwin-apple-i686-dev3-20061004.tar.gz To install it, copy it to /Applications, and then: tar zxvf freesurfer-Darwin-apple-i686-dev3-20061004.tar.gz To setup: setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh This distribution is from our 'dev' (development) code base, so it is slightly different from the normal publicly distributed 'stable' release. A stable build release of this Intel Mac distribution (with associated install GUI) will coincide with the next stable build release (next month, hopefully). Nick

2 2

volume won't load in tkregister (fwd)
by Akram Bakkour 30 Nov '06

30 Nov '06

Hi, I'm on thigpen and I ran source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/thigpen/8/users/akram/ADNI_processing tkregister2 --mgz --s 023_S_0030 --fstal but no volume will load. Any suggestions? Thanks! Akram. > > -- --------------------------------------------------------------- Paul Raines email: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129 USA

2 1

FSGD and design matrix
by Reschke, Cole 30 Nov '06

30 Nov '06

All- I am looking to run freesurfer group analysis on a longitudinal study, examining the changes between baseline and follow-up. I would like to set up a paired t-test, yet I am still in need of some assistance creating my FSGD file and my design matrix. I have read the GroupAnalysis wiki page, and did not see anything regarding t-tests. Also, is "Class" is equivalent to "Group" in the FSGD file? I have been using your sample GroupDescriptorFile to create my own, and pasted an excerpt below (my edits are in red and underlined). GroupDescriptorFile 1 Title MyTitle Class bsl plus blue Class flp circle green Variables Age Gender Input subjid1 bsl 20 M Input subjid1 flp 20 M DefaultVariable Age Cole Reschke Data Manager, PET Center Banner Alzheimer Institute Banner Good Samaritan Medical Center Phone: (602) 239-4868

2 1

segmentation fault during mri_glmfit
by Bum Seok Jeong 30 Nov '06

30 Nov '06

Dear freesurfer users I got an error message during mri_glmfit. (please see below my error message) I was able to find 'mri_glmfit.log' file in './glm/lh.dx_age.glmdir' directory Thank you for advance --------------------------------------------------- These are my constrasts. : to construct the contrast vector for testing volume change according to age = age.mat 0 0 0 1 : for effect of interest (ANOVA: f test) -> Am I right? 1 0 0 0 0 1 0 0 0 0 1 0 : for difference btw 3 group independent of age -> Am I right? -1 0 1 0 0 -1 1 0 There are three class and one variable (see below my FSGD file) # FSGD file GroupDescriptorFile 1 Title Thickness vs Dx and Age Class A circle blue Class B circle green Class C plus red Variables Age Input 61 A 71 Input 54 A 72 Input 12 B 74 Input 33 B 77 Input 63 C 80 Input 01 C 87 ...... DefaultVariable Age # Error message mri_glmfit --y lh.dx_age.thickness.10.mgh \--fsgd my_dx_age_1_fsgd.txt doss \--glmdir lh.dx_age.glmdir \--surf average lh \--C age.mat gdfReadHeader: reading my_dx_age_1_fsgd.txt INFO: ignoring tag vs INFO: gd2mtx_method is doss Reading source surface /GR/average/surf/lh.white reading group avg surface area 936 cm^2 from file Reading in average area /GR/average/surf/lh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 62167.195312 AvgVtxArea 0.379434 AvgVtxDist 0.717000 StdVtxDist 0.244431 $Id: mri_glmfit.c,v 1.83 2006/03/10 23:26:51 greve Exp $ cwd /GR/group_analysis/glm cmdline mri_glmfit --y lh.dx_age.thickness.10.mgh --fsgd my_dx_age_1_fsgd.txt doss --glmdir lh.dx_age.glmdir --surf average lh --C age.mat sysname Linux hostname *** machine x86_64 user *** FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /GR/group_analysis/glm/lh.dx_age.thickness.10.mgh FSGD my_dx_age_1_fsgd.txt glmdir lh.dx_age.glmdir Creating output directory lh.dx_age.glmdir Loading y from /GR/group_analysis/glm/lh.dx_age.thickness.10.mgh Matrix condition is 177.843 search space = 93594.7 Segmentation fault

2 1

error message during CA normalize (3T image)
by Bum Seok Jeong 30 Nov '06

30 Nov '06

I'm trying to analyze 3T spgr image with freesurfer. I faced error message during autorecon2 step. And typed 'recon-all -autorecon2 -conorm -subjid case**** to figure out which process it occured in. This is error message after putting '-conorm' tag. ------------------------------------------------------------------------------------ ..... registration took 7 minutes and 3 seconds. #-------------------------------------- #@# CA Normalize Thu Nov 30 11:12:00 EST 2006 /gr/caseD00916/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... GCAhistoScaleImageIntensities: could not find wm peak reading input volume from nu.mgz... resetting wm mean[0]: 109 --> 116 resetting gm mean[0]: 68 --> 68 input volume #1 is the most T1-like using real data threshold=39.0 using (126, 155, 152) as brain centroid... mean wm in atlas = 116, using box (126,155,136) --> (125, 154,168) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Linux 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22:53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Nov 30 11:12:16 EST 2006

2 1

ASL perfusion maps
by Abi Gopal 30 Nov '06

30 Nov '06

Hi all I have collected some raw Arterial Spin Labeling (ASL) data. I would like to use freesurfer to create perfusion maps of this data. Is it possible to take the raw data, motion correct it, perform a pairwise subtraction, and then average all the subtractions to create a mean perfusion map? Please let me know if you have ideas on how to do this sort of thing. Thanks Abi -- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School

3 3

Extracting surface normals using mri_surf2surf
by XJ Kang 29 Nov '06

29 Nov '06

Hi, All, I am trying to extract the surface normal values using mri_surf2surf: %mri_surf2surf --s subject1 --hemi lh --sval-nxyz white --tval lh.white.surfn.img --trg_type analyze4d The error mesage is : ...... Loading source data Extracting surface normals INFO: surfcluster: NOT fixing group surface area INFO: trgsubject = srcsubject Saving target data Reshaping 131441 (nvertices = 131441) ANALYZE FORMAT ERROR: nslices 131441 in volume exceeds 32768 I am using FreeSurfer v303. I tested the above command on the subjects inflated by old version of FreeSurfer, and I could get the surface normals. Anything wrong with the new inflation? Thank you for your time. XJ Kang

3 3

mri_segstats - missing data in FreeSurferColorLUT.txt
by Darren Weber 29 Nov '06

29 Nov '06

Why do we see the error below from CTABread? Is it important to have 6 parameters in FreeSurferColorLUT.txt? Thanks, Darren mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject ucsf_disc08 Using defalt ctab /home/dweber/freesurfer/home/FreeSurferColorLUT.txt atlas_icv = 1.3356e+06 Loading mri/aseg.mgz Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1453903 # brainmaskvolume 1453903.0 # nbrainsegvoxels 1047830 # brainsegvolume 1047830.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids CTABread(/home/dweber/freesurfer/home/FreeSurferColorLUT.txt): could not scan 6 parms from line 1100 ctx-lh-Unknown 0 0 0 (403) CTABread(/home/dweber/freesurfer/home/FreeSurferColorLUT.txt): could not scan 6 parms from line 1101 ctx-lh-Corpus_callosum 50 50 50 (403) ....

2 1

re: group analysis
by Emily Cooper 27 Nov '06

27 Nov '06

Hi Doug, Thanks! I was wondering: when I have selected "Calculate Identity Matrix" to overly functional data on the fly in the tksurfer gui before, it seems to align it perfectly to the freesurfer anatomical. Is there a way to output the matrix that it's using as a register.dat file? I was trying last week to make the file using tkregister2 and for some reason it always came out misaligned (that's why I started just using the gui). mri_vol2surf is working to make surface overlays, but they don't line up right, presumably because it's using the old register.dat file from tkregister2. mri_vol2surf --src 003/bold/03.trim_time.tval+orig.BRIK --src_type afni --srcreg register.dat --hemi lh --projfrac .3 --out trim_time.tval.surf.5 --out_type paint Emily

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer November 2006