Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

symbolic links
by bdragans＠uke.uni-hamburg.de 01 Dec '06

01 Dec '06

Hi Doug, while trying to expand the volume of my virtual machine to be able to create symbolic links I started wondering if the way I preprocessed my data with recon_all might be affected somehow by the fact symbolic links were not supported (the data was located on a mounted drive). The only error message regarding this came during the make_average_subject part... Is there any way to use freesurfer avoiding the creation of symbolic links? many thanks bogdan

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Morphometric indices of the hippocampus
by Juergen Haenggi 01 Dec '06

01 Dec '06

Dear Freesurfer users I tried to compute the hippocampal volume with the following command: mri_label_volume <volume> <label 17> <label 18> but which is the most appropriate volume to label? Is there also an opportunity to measure thickness and surface area of the hippocampi? I had run recon-all -all, but cannot find the results for the hippocampus in the file! Thanks in advance Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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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

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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

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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

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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

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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

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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

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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) ....

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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

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