Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

surface group analysis design matrix question
by Charlotte Bernard 22 Feb '12

22 Feb '12

Dear freesurfer users, I have a question about a design matrx. I have read all your explications about the FSDG file. But I am not sure I can construct the design which corresponds to my study! I have two groups: control and patients. I want to compare their cortical thickness. I have have one continue covariable (age) and three categorial covariable (gender, educational level and laterality). The educational level has five levels. Is it possible to construct such design matrix? Thanks for all, Charlotte

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weird relabeling with mri_convert
by David Grayson 21 Feb '12

21 Feb '12

Hi freesurfer folks, I am using mri_convert to reorient my custom cortical parcellation (a nifti file generated from an annotation file), and I have run into some unexpected blips with some seemingly errant reindexing. Here is the command I am using: mri_convert -rl FREESURFER/mri/orig/001.mgz -rt nearest FREESURFER/label/ROIs_custom.nii.gz -nc reorient/ROIs_custom_reorient.nii.gz For the most part, this works well for most of the indices. The biggest problem is that the highest value index (2063) is being completely relabeled in ‘ROIs_custom_reorient.nii.gz’ with several smaller values in the 20’s range. But this occurs to a smaller extent with many of the other regions as well, where small parts of those regions are being relabeled with values anywhere from 1 to 20. Can anyone give me some insight as to what’s up with this and what I might be able to do to fix it? Thank you very much for any help. -David

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mri_vol2vol not downsampling when applying a morph and a rigid registration matrix
by Alex Kell 21 Feb '12

21 Feb '12

Hi Freesurfers, I am struggling to get mri_vol2vol to downsample when I apply an inverse morph and an inverse registration matrix. Specifically, I am bringing a volume in cvs_avg35 space back into an individual subject's functional space. I have already registered the subject's functional to their anatomical using bbregister and registered the subject's anatomical to cvs_avg35 space using mri_cvs_normalize. Here is the mri_vol2vol call that I am using to move a volume from cvs space to native functional space: mri_vol2vol --targ $roi_in_cvs_space \ --mov $func_vol_file \ --reg-final $bbreg_file \ --inv \ --inv-morph \ --m3z $morph_file \ --o $roi_in_native_func_space \ --interp nearest \ --noDefM3zPath This call seems to register the cvs space to the native functional space accurately -- the mask that I am projecting is in a reasonable position in the functional space. However, the voxel size for this output volume is not the same size as the functional voxels. The voxel size is still the same as the size in cvs space. (Or it could be the anatomical space, since both are 1 mm isotropic.) My question: How do I get mri_vol2vol to downsample? I have no problem getting mri_vol2vol to downsample from native anatomical to native functional by applying the inverse of the bbregister-generated matrix, but I am struggling to get the appropriate downsampling here. Any suggestions? And FYI: I'm using this version of freesurfer: freesurfer-Linux-centos4_x86_64-dev-20120104. Thanks in advance! Best, Alex Kell Kanwisher Lab Manager

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HELP!A problem of Oracle VM VirtualBox
by bowang21＠mail.ustc.edu.cn 21 Feb '12

21 Feb '12

Dear Guys: Now I'm learning Freesurfer and suffering some troubles.I just installed the Oracle VM VirtualBox and virtualitied a virtual computer with "freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full". When I started the virtual computer and wanted to mount disk partition (eg: F) to this virtual computer.But the system warned that "mont only root can do".What was worse, I could not log in root,because password is required. Even I could not reset the password. Now I'm in trouble.I need your help. Thanks! Best wishes. Yours sincerely BoBo

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Overlaying a lesion map onto an inflated surface
by Catherine Wan 21 Feb '12

21 Feb '12

Dear Freesurfer list, I did a group level thickness analysis in qdec with lesioned brains and I would like to overlay individual lesion map onto the group level results to check for overlap, etc. I was wondering if I could convert individual lesion maps and overlay them on the group level inflated surface in qdec. I've tried bbregister, and mri_vol2surf, and mri_convert, but none of them seemed to work. Many thanks in advance. Catherine

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ASEG, APARC reliability
by Alan Francis 21 Feb '12

21 Feb '12

Dear Bruce: I ran 3 brains twice and checked the ASEG and APARC values for each of these. It turns out that the ASEG values are exactly the same - both times, while the APARC values differ. Could you please explain why this happens. thanks so much ~ Alan Beth Israel Deaconess Medical Center

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Crossing surfaces in parcellation in hippocampus?
by Charlotte Bernard 21 Feb '12

21 Feb '12

Dear freesurfer users, I am a new user of Freesurfer. I have a question about the parcellation: in my data, I am checking the pial and white surfaces of brains. I have observed on my subjects that surfaces are crossing in the hippocampus. I don't understand why the pial and white matter surfaces cross in that region! Is it normal? Is it use for calculating thickness? Is their a mean to fix that problem? Thanks for your help, Charlotte

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TRACULA question: pathstats.byvoxel.txt
by Minjie Wu 20 Feb '12

20 Feb '12

Hello Tracula Developer & User, I found a few subjects have pathstat.overall.txt information but with blank voxel information in pathstats.byvoxel.txt. For such tracts, they usually len_min = len_max = len_avg. Anyone know what happened for the fiber tracking? Is it possible to extract the byvoxel information along the tract? Thanks, Minjie For example: [minjiewu@ccmfsl1 data]$ more 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt # Title Pathway Statistics # # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats # cvs_version # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr --dtbase /ccm/pavuluri/rest/DTI/data/223 31/dmri/dtifit --path rh.slfp --subj 22331 --out /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt --outvox /ccm/pavuluri/rest/DTI/data/ 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.byvoxel.txt # sysname Linux # hostname ccmfsl2.psych.uic.edu # machine x86_64 # user minjiewu # anatomy_type pathway # # subjectname 22331 # pathwayname rh.slfp # Count 1000 Volume 86 Len_Min 86 Len_Max 86 Len_Avg 86 Len_Center 0 AD_Avg 0.00112029 AD_Avg_Weight 0.00112029 AD_Avg_Center nan RD_Avg 0.000783836 RD_Avg_Weight 0.000783836 RD_Avg_Center nan MD_Avg 0.000895987 MD_Avg_Weight 0.000895987 MD_Avg_Center nan FA_Avg 0.264347 FA_Avg_Weight 0.264347 FA_Avg_Center nan

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optic nerve inlcuded as pial matter
by Julia Hill 20 Feb '12

20 Feb '12

Good morning, I have a question about editing of the pial. I have noticed that on every single scan (so well over 100), the optic nerve has been included as pial matter (see attached screenshot). This occurs from between 5 and 10 slices in length. Will i need to remove the voxels from every scan, and do a recon-all autorecon2-pial? Thank you kindly in advance, Julia Hill Julia Hill Research Assistant School of Psychiatry University of New South Wales Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268

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Does the SurfArea in the lh.aparc.a2009s.stats calculated based on white matter surface or pial surface
by ZhiLiangLong 20 Feb '12

20 Feb '12

Hi, all Does the SurfArea in the lh.aparc.a2009s.stats, as presented below(red color), calculated based on white matter surface or pial surface? any suggestions appreciated. # TableCol 10 Units unitless # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd G_and_S_frontomargin 1518 988 2359 2.111 0.655 0.176 0.120 48 7.0 G_and_S_occipital_inf 1831 1257 3077 2.091 0.586 0.182 0.077 40 5.8

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Freesurfer February 2012