Freesurfer

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19 participants
30088 discussions

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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optimal parcellation example
by Keefe, Helen L 20 Feb '12

20 Feb '12

Does anyone have a template/atlas/graphic showing what the optimal parcellation should look like, with the areas labeled? I'm particularly interested in medial "Show Main Surface" view after running tksurfer - but would also like inflated and other orientations as well if anyone has them On medial I am especially interested in the boundary between rostralanteriorcingulate - medialorbitofrontal and lingual - pericalcarine - cuneus Thanks, Helen ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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overlay question
by LAOUCHEDI MAKHLOUF 20 Feb '12

20 Feb '12

hi all excuse me for this "simple question" but i am quiet new to freesurfer (i use it just for the parcellations). i've some functionnal maps (i've used spm for that) that i want to use as an overlay on the pial surface of the subject. is there an easy way to do it thanks

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freesurfer license file
by Christopher Bell 19 Feb '12

19 Feb '12

How do I obtain a freesurfer license file?

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