Freesurfer February 2010

freesurfer@nmr.mgh.harvard.edu

96 participants
153 discussions

cross-sectional analyis error
by Guang Zeng 18 Feb '10

18 Feb '10

Hi, there, I am testing two subjects using cross-sectional FS. Both of they have being processed for almost four days. Both of them are stuck at the mris_fix_topology step, but there is no error message pops up. Subject#1 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ before topology correction, eno=-132 (nv=182824, nf=365912, ne=548868, g=67) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 71554 ambiguous faces found in tessellation segmenting defects... 39 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 22 into 9 -merging segment 29 into 27 37 defects to be corrected 0 vertices coincident reading input surface /data1/radiology/m047599/subjects/027_S_0408_20060510/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2222 (-4.6111) -vertex loglikelihood: -6.1352 (-3.0676) -normal dot loglikelihood: -3.5992 (-3.5992) -quad curv loglikelihood: -5.8849 (-2.9424) Total Loglikelihood : -24.8415 CORRECTING DEFECT 0 (vertices=30671, convex hull=1376) ************************************************************* Subject#2 ************************************************************* Correcting Topology of defect 2 with euler number 1 (0 loops) Nothing to correct for defect 2!! AFTER CORRECTION, EULER IS -262 Surface Diagnostics: eno=-262 (nv=157710, nf=315944, ne=473916) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Correcting Topology of defect 3 with euler number -219 (110 loops) computing statistics for defect 3: 23911 vertices location: [ (168,58,111) - average intensity = 83.612 ] -gray ( 77.29 , 6.14 ) -white ( 93.87 , 3.59 ) -gray ( 79.92 , 20.78 ) -white ( 95.75 , 18.72 ) -intensity (77.286301 [log = -2.730186 ]- 93.865768 [log = -2.235836 ]) -curv (k1=-0.170 (0.615) , r1 = 5.894 | k2=-0.052 (0.142), r2 = 19.402 ) -curv (k1=-0.138 (0.656) , r1 = 7.230 | k2=-0.024 (0.219), r2 = 41.547 ) max face = 47468(47468) - loop = 1 (110) - ntries = [18,18997] BEST FITNESS (o)is -9.95545 mri =0.000 curv = 0.865 unmri = 6.496 ( f=0.00 , v=0.00 , c=0.86 , q= 1.73 ) ( f=0.00 , v=0.00 , c=0.86 , q= 1.73 ) BEST FITNESS (M) is 14.81362 mri =0.000 curv = 0.886 unmri = -18.358 ( f=0.00 , v=0.00 , c=0.89 , q= 1.77 ) ( f=0.00 , v=0.00 , c=0.89 , q= 1.77 ) Could any one tell me how to fix this problem, is there a method to ignore this fix_topology step? Thanks! Guang _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/

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Paradigm file question
by John Richey 18 Feb '10

18 Feb '10

Dear Freesurfer experts, For the first column in paradigm (.par) files in fsFAST, is it necessary for the stimulus onset times to be cumulative across runs? In other words, if I present the same task N times in run 001, run 002, ... run N, is it necessary for the second through Nth .par file to indicate the cumulative time elapsed? Or should each .par file start with time = 0?

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converting nifti to .mgz files - command
by Jenessa Price 18 Feb '10

18 Feb '10

Can you please tell me the exact mri_convert command for converting nifti to .mgz? We had originally done it using .img/.hdr files, but there were errors with the recon because the orientation wasn't correct. We then were able to get a correct orientation using the .nii format but could not convert to .mgz with the mri_convert command. Thank you! -- Jenessa S. Price, B.A. Graduate Student, Clinical Psychology and Neuropsychology University of Cincinnati

4 3

Color Scale in tksurfer
by Oya, Hiroyuki 17 Feb '10

17 Feb '10

Dear All, How can I use my own color scale in tksurfer overlay? Thank you in advance? Hiroyuki

1 0

lobe volumes...
by Gonzalo Rojas 17 Feb '10

17 Feb '10

Hi: How can I get the volume of each lobe ?... each hemisphere ?... Sincerely, Gonzalo Rojas Costa

2 1

Wmparc zero volumes
by Lena Palaniyappan 17 Feb '10

17 Feb '10

I want to extract wm volumes using wmparc for parcellations contained in Destrieux 2009 atlas but when I inspect my wmparc stats file, most of the volumes that I am interested in are reported as zero. What should I do to read these volumes? Many thanks Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

3 2

Surface-based inter-subject registration of both anatomical and functional images
by Joonkoo Park 17 Feb '10

17 Feb '10

Hi, I'm completely new to FreeSurfer, and I'd like to get some guide to surface-based inter-subject registration in analyzing some fMRI data. I have an anatomical image (e.g. t1-spgr or mprage) and functional images (e.g. epi) in NIFTI or ANALYZE format for each subject. In each subject's native space (typically using SPM), I perform some GLM and get some statistical parametric maps (SPMs) for each subject (note that the anatomical image and the resulting functional image are co-registered). Now, I'd like to use the surface-based normalization (or I realized that this procedure is called registration in the freesurfer community) procedure to normalize the anatomical and the functional images to a standard space. Could you please guide me what steps I need to perform in order to achieve this goal? Here are some specific questions: 1. What command shall I use to get the nifti/analyze images into the freesurfer format? I was wondering if recon-all is really necessary. I heard that it takes more than a day to do one subject, and I don't think I need all those results for my purpose. 2. I found that the command "mris_register" will give me what I want at least for the anatomical data. But how do I do the same for the functionals? Also, how will I make sure that my anatomicals and functionals are co-registered? 3. I need to be able to get into the data structure after inter-subject normalization. For the nifti/analyze files, there's an SPM command that will bring all the data into a matrix in Matlab. But for the freesurfer format, is there a way to import the surface-based files into Matlab so that I can play with the output data? I may not be asking in the right order or even in the right way. But I'm thinking that any FreeSurfer guru should be able to help me. I searched through the archive and the documentations but wasn't satisfactory. Thanks in advance! Joon -- Joonkoo Park Ph.D. Candidate, Cognition & Cognitive Neuroscience Department of Psychology, University of Michigan

3 2

difference between structures...
by Gonzalo Rojas Costa 17 Feb '10

17 Feb '10

Hi: There exist any tool that could show me the structures that differ between each hemisphere more than a given percentage (volume) ?... For example: the hippocampus... Sincerely, Gonzalo Rojas Costa

2 1

question about visualization of negative activation
by Balaji Goparaju 17 Feb '10

17 Feb '10

Hello, I have a loaded a significance map using the tksurfer-sess command. I want to visualize only the negative activation on the surface. In the View -> Configure -> Overlay window, I check both the "truncate" and "inverse" buttons. So only the negative activation is shown however it is in Red-Orange-Yellow color scale. How can I get this negative activation to be represented by Dark and Light Blue color scale. Thanks in advance for the help! Balaji Goparaju

2 1

Bbregister
by Lena Palaniyappan 17 Feb '10

17 Feb '10

I want to use contrast files that are outputs from SPM (in IMG HDR format) to overlay on inflated surfaces. But if I use bbregister and choose T1 as the image type, the regisration achieved is poor (image attached) Is this the correct way of doing this or am I missing something? Commands used: bbregister --mov con_0001.img --t1 --s fsaverage --init-spm --reg register.dat cat register.dat tkregister2 --mov con_001.img --reg register.dat --surf Many thanks Lena This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Freesurfer February 2010