Freesurfer June 2009

freesurfer@nmr.mgh.harvard.edu

94 participants
140 discussions

Installing FreeSurfer on iMac running Xubuntu
by Lucas Eggert 05 Jun '09

05 Jun '09

Dear List, I am trying to install FreeSurfer on an iMac on which I am using Ubuntu 9.04 (jaunty). I downloaded the CentOS 4x86_64-tar.gz file, moved it to '/usr/local/' and unpacked it there ('tar xzvf ...'). I saved the .license-file in '/usr/local/freesurfer'. Trying for example 'mri_convert', throws the following error-message: 'bash: /usr/local/freesurfer/bin/mri_convert: cannot execute binary file' What is my mistake? Any help would be very much appreciated! Thanks! All the best, -Lucas

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export skull stripped images
by Jose Luis Cantero Lorente 04 Jun '09

04 Jun '09

Dear Freesurfers, is it feasible to save to nii the MR images after stripping the skull in Freesurfer? If so, please let me know how to do it. Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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Re: 'Max' in sig.cluster.summary
by Judith Segall 04 Jun '09

04 Jun '09

Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output. Is the " Max" in column 2 below a measurement of thickness? If it is thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region. The max vertex in that cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations? If it does not refer to thickness, is it a statistic, etc? # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal I am trying to finish writing up my results and just need answer to this question to continue. Thanks, Judith S. Mind Research Network

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scan orientation matter?
by David Qixiang Chen 04 Jun '09

04 Jun '09

Hi all,Just wondering if the scan orientation for input DICOMs matter. I know that Analyze format does not preserve left/right orientation information, but would a saggital DICOM scan have the same problem? We have a lot of axial scans, would incorporating freesurfer subjects with saggital scans in our comparisons cause any problems? Assuming that the slice thickness is 1mm with 0 spacing at 3T, with 256x256 res. We are using GE Signa HDx scanners. Thanks - David Qixiang Chen

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question about wmparc stats files
by Dana W. Moore 04 Jun '09

04 Jun '09

In my wmparc.stats file I have noticed that for many structures I am just getting a value of 0. I do get output for ctx and wm values corresponding to the aparc structures and for subcortical structures corresponding to the aseg.stats file. However, towards the end of the document, there is a whole list of structures with 0 for volumes (e.g. internal capsule, thalamic regions). Why am I not getting any output for these regions? I have attached a wmparc.stats file for reference. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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"smooth sulc on only part of the surface" one more time
by Zhangyuanchao 04 Jun '09

04 Jun '09

Hi, experts, I am interested in only the positive sulc and would like to make group analysis of the postive sulc values. Hence I would like to mask off the negative values (as the lh.sulc file has both positive and negative value). Before making group analysis, I have to resample and smooth the sulc value. How do I smooth the positive sulc in a way that the negative sulc values will not have an effect on the smoothing process? Example if I smooth the positive sulc directly with the negative values, it will have some effect on the positive values since gyri and sulci are alternating. you suggest me using mri_binarize and mri_fwhm to make a mask and smooth it with a mask. As suggested, I have done so. However, there is a problem I can not tackle. Using mri_binarize --i lh.sulc --min 0 --o lh.such.mask.mgh When I read the lh.such.mask.mgh into matlab so that I can see the data inside. To my surprise, I saw a vector which contains nearly all 0's except some very small numbers like 1.401298464324817e-45, not binary file which contains only 0's and 1's. I further tried: mri_binarize --i lh.sulc --min 0 --o lh.such.mask.mgh --binval 1 It has the same problem as above. After launching: mris_fwhm --i sulc --subject Ad001 --surf white --mask lh.such.mask.mgh --hemi lh --fwhm 20 --o lh.sulc.mgh I read lh.sulc.mgh into matlab, it contains all 0's. I read the mgh file using Keith worsley's SurfStatReadData function. I do not know where it is wrong. Thank doug for your helpful suggestions! Thank you very much! yuanchao ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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Measurement voxel space
by Ed Gronenschild 04 Jun '09

04 Jun '09

Hi, To which voxel space (native, Talairach or any other standard space) do the measured cortical thickness and areas/volumes in the statistical output files refer? Ed

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multiple subjects on Linux
by Barnali Basu 03 Jun '09

03 Jun '09

Experts, I have 13 subjects on which I have to run autorecon-all processes to do cortical reconstruction. I work on an Ubuntu machine, dual core, each with 2.8 GHz and 4 MB RAM. Can I run more than one subject simultaneouly? If yes, how many and in what way? Would that affect process time? Your suggestions will be appreciated Thanks and regards -- Barnali Basu

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smooth sulc on only part of the surface
by Zhangyuanchao 03 Jun '09

03 Jun '09

Hi,all I am interested in only the positive sulc and would like to make group analysis of the postive sulc values. Hence I would like to mask off the negative values (as the lh.sulc file has both positive and negative value). Before making group analysis, I have to resample and smooth the sulc value. How do I smooth the positive sulc in a way that the negative sulc values will not have an effect on the smoothing process? Example if I smooth the positive sulc directly with the negative values, it will have some effect on the positive values since gyri and sulci are alternating. If I set all the negative value to be 0 and leave the positive value unchanged, it will also have an effect on the positive value, but to a less degree. Would the latter method be a feasible and valid way to smooth the positive sulc or is there better way for me to smooth the positive sulc and make a group analysis of just the positive sulc values? Thanks! yuanchao ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

2 1

substantia nigra's segmentation
by Paula Diniz 03 Jun '09

03 Jun '09

Hello! How I do for make segmentation of substantia nigra using freesurfer? Thanks! -- ================================== Paula Rejane Beserra Diniz Bacharel em Informática Biomédica Mestre em Neurociências Doutoranda em Neurociências Universidade de São Paulo Hospital das Clínicas - Ribeirão Preto ==================================

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Freesurfer June 2009