Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30097 discussions

FW: How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory?
by Boric, Katica A. 26 Aug '13

26 Aug '13

________________________________________ From: Boric, Katica A. Sent: Monday, August 26, 2013 4:02 PM To: Douglas N Greve Subject: RE: [Freesurfer] How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory? Hi Doug! Thanks for getting back so fast! I did the registration but I only got this email: Here is your FreeSurfer license. Place the three lines between the CUT HERE markers in a file named ".license" in the directory pointed to by the $FREESURFER_HOME environment variable (see the FreeSurfer documentation). #---------------CUT HERE--------------- kboric(a)partners.org 16851 *C9NanJsRCd7o #---------------CUT HERE--------------- and this is where I am stuck.... don't know how to procede! Thanks again, Katica ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Sent: Monday, August 26, 2013 3:59 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory? Hi Katica, on that page there is a link to the registration page. Once you register (free), you will be given a .license file doug On 08/26/2013 03:22 PM, Boric, Katica A. wrote: > Hello! > I am new to free surfer and Linux and I am having installing free > surfer. I am using Fedora on a VMware workstation > I successfully (I think) downloaded it and installed it following the > instructions (https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) > But now I am stuck trying to copy the three lines of the license info > to the file .license. > Any advice? > Thank you very much, any help is appreciated it! > > Katica > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FDR in different hemispheres
by Emily Boeke 26 Aug '13

26 Aug '13

Hi Freesurfers, I have a contrast that produces comparable activation in both hemispheres. But when I set the threshold using FDR in the Configure Overlay Display window, the threshold is set to 5.1 for left hemisphere and 3.3 for the right hemisphere, leaving significant clusters only in the right hemisphere. Does someone know why the FDR threshold would be so different between the two hemispheres? Thanks! Emily

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How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory?
by Boric, Katica A. 26 Aug '13

26 Aug '13

Hello! I am new to free surfer and Linux and I am having installing free surfer. I am using Fedora on a VMware workstation I successfully (I think) downloaded it and installed it following the instructions (https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) But now I am stuck trying to copy the three lines of the license info to the file .license. Any advice? Thank you very much, any help is appreciated it! Katica

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Freesurfer Editing Strategy
by Khadka, Sankalpa 26 Aug '13

26 Aug '13

Dear freesurfer experts, I have a question about making edits in the freesurfer results. During the workshop which I attended this year, I learned about white matter edits and control points edits when white matter is not segmented accurately. I have used these tools quite successfully in our projects. However, in our research in multiple sclerosis, often times we encounter cases with lesions on grey matter. The lesions in grey matter causes intensity of the voxel over that region to become hypo-intense like CSF. Due to this, the pial surface line is pushed inward into the lesion, missing some grey matter around it. Since, cortical thickness is the most important measure in our research, we could like to be able to solve this issue. We would like to make sure that the pial surface line goes around the lesion without missing grey matter for accurate thickness calculation. In order to solve this issue we have tried to first delelte and fill the lesion in the brainmask.mgz with voxels with grey matter intensity in the region using the voxel editing tools (instead of 255(default) used in white matter edit, we use 70-75 for grey matter). After editing, we run recon-all with autorecon-2 and autorecon-3. Quite surprisingly, this strategy has not resolved our problem. My understanding is that the pial and main surface lines (red and yellow) were draw based on the intensity of voxel. Our question is, why would the lesions which are now filled with grey matter not treated as grey matter? We have tried this strategy, and it has not worked. What would you recommend us for solving such issue? I have attached a screen shot of a slice where you can notice that in the top right corner, the lesion on the grey matter causes the pial surface line to miss grey matter around it. Ideally, we would like the pial surface line to go around the normal grey matter surface. Thank you, Sankalpa Khadka Research Assistant Neurolgy, Yale School of Medicine

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regarding adding and deleting voxels in wm.mgz and brainmask.mgz
by Mehul Sampat 26 Aug '13

26 Aug '13

Hi Folks, I see on the tutorial websites that when voxels are added to wm.mgz or brainmask.mgz, the new voxels are given a value of 255; while when voxels are deleted, these locations are set to 1. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits Can the deleted voxels can be set to 0 or they have to be set to 1; Or is 0 used to differentiate the background voxels from brain voxels ? Thanks Mehul

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Postdoctoral Fellow (neuroimaging) in Aging
by Ayaz, Muhammad 26 Aug '13

26 Aug '13

Postdoctoral Fellow in Neuroimaging (MRI)/Cognitive Aging Area Cerebrovascular Laboratory Department Institute for Exercise and Environmental Medicine Institution The University of Texas Southwestern Medical Center of Dallas Job Description The applicant should have a Ph.D. and/or M.D. degree. Experience and previous training in MRI and image data analysis are required. Previous experience with Freesurfer, FSL, AFNI, MATLAB, SPM is desired. UTSW has an advanced imaging research center equipped with state-of-the-art MRI systems dedicated to research (Two 3 T and one 7T whole-body human MRI unit). The applicant will have an opportunity to work in a highly collaborative research environment with exposure to the cutting-edge research in neuroimaging (MRI/PET), cognitive neuroscience and human physiology. The ideal candidate should have a strong publication record and excellent communication and laboratory skills. She/he will work on a NIH funded project to study the impact of aerobic exercise training on arterial aging, brain perfusion, structure and cognitive function in human subjects. Salary is commensurate with experience according to NIH stipend levels. The fellow will be an employee of both UT Southwestern Medical Center and Texas Health Presbyterian Hospital and will receive comprehensive fringe benefits. If interested please send your CV to, - - - - - - - - - - M. Ayaz Khan, PhD Research Fellow Institute for Exercise and Environmental Medicine Texas Health Presbyterian Hospital Dallas Department of Internal Medicine and Cardiology University of Texas Southwestern Medical Center 7232 Greenville Avenue, Suite 435, Dallas, TX 75231 phone: 214.345.4639 | fax: 214.345.4618 MuhammadAyaz(a)texashealth.org> MuhammadA.Khan(a)utsouthwestern.edu The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

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Final call for special issue: 'Functional brain mapping of epilepsy networks: methods and applications'
by David Abbott 26 Aug '13

26 Aug '13

Hello, Please be advised that a call for papers is closing in one week (Monday September 2, 2013, with a final paper submission deadline of 1st February 2014) for the Frontiers in Neuroscience and Frontiers in Neurology Research Topic: 'Functional brain mapping of epilepsy networks: methods and applications'. This is a parallel topic across two journals: Frontiers in Neuroscience (section: Frontiers in Brain Imaging Methods<http://www.frontiersin.org/Brain_Imaging_Methods/researchtopics/Functional_…>) for papers with a methodological focus, and Frontiers in Neurology (section: Frontiers in Epilepsy)<http://www.frontiersin.org/Epilepsy/researchtopics/Functional_brain_mapping…>for papers with an application or clinical focus. You may click on the links above for further information. Frontiers journals are open access. Publication fees are substantially reduced for papers included in a Research Topic. Researchers from most leading epilepsy imaging labs have already confirmed their participation in this topic. Proposals (in the form of a max. 1 page abstract or outline) should be submitted by 2nd September 2013. If the abstract is accepted, then the associated paper can be submitted at any time up until 1st February 2014. Thus some papers in the topic may be published before the final submission deadline. Regards, David. --- David Abbott, PhD Senior Research Fellow (Physics & Neuroinformatics), Brain Research Institute, The Florey Institute of Neuroscience and Mental Health Honorary Senior Fellow, Department of Medicine, The University of Melbourne. Address: Melbourne Brain Centre - Austin Campus, 245 Burgundy Street Heidelberg, Victoria, 3084, Australia.

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mri_convert command
by 沈庄明 25 Aug '13

25 Aug '13

Hi everyone, I'm new to FreeSurfer. I'm so confused with the difference between mri_convert --in_orientation and mri_convert --out_orientation. Do they all reslice the volume? How do they modify the header files of the volume? I wish someone could explain the difference between them in detail. Thanks! Zhuangming Shen

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Re: [Freesurfer] fcseed-sess error
by Omar Singleton 24 Aug '13

24 Aug '13

Sorry about that. I must have clicked 'reply' by mistake rather than 'reply all'. I wouldn't want to deprive anyone of the opportunity to help me resolve this issue. --The issue-- I looked at the segmentation in tkmedit and the labels for the ventricles showed up the same as in subjects that worked. I checked registration by eye and used this command from the tutorial: tkregister-sess -s AC30_1319 -fsd Bold1 -per-run -bbr-sum Which output: AC30_1319 001 0.4437 I'm not sure what the problem is with these subjects. Is there another way I should check the data? Any suggestions? -Omar > Hi Omar, can you post questions to the list instead of us personally? > thanks! > doug > > On 08/19/2013 09:41 AM, Omar Singleton wrote: >> Hi Doug, >> >> Thanks for the help. I looked at the segmentation in tkmedit and the >> labels for the ventricles showed up the same as in subjects that worked. >> I >> checked registration by eye and used this command from the tutorial: >> >> tkregister-sess -s AC30_1319 -fsd Bold1 -per-run -bbr-sum >> >> Which output: >> >> AC30_1319 001 0.4437 >> >> I'm not sure what the problem is with these subjects. Is there another >> way >> I should check the data? Do you have any other suggestions? >> >> Best, >> Omar >> >>> Hi Omar, it is not finding any ventricle voxels. Check the FS >>> segmentation to make sure that the ventricles are labeled and also >>> check >>> the registration to make sure it looks ok. >>> doug >>> >>> >>> On 8/14/13 12:04 PM, O S wrote: >>>> Dear Support, >>>> >>>> I am trying to use fcseed-sess to create a ventricle and CSF regressor >>>> for >>>> my resting state analysis. I have encountered an error running >>>> fcseed-sess. >>>> >>>> fcseed-config -vcsf -fsd Bold1 -mean -cfg vcsf_bold1_config -overwrite >>>> >>>> works, but then the following command fails: >>>> >>>> fcseed-sess -s AC30_1319 -cfg vcsf_bold1_config -overwrite >>>> >>>> The above command worked for half my subjects and had the below error >>>> for >>>> half with no discernible pattern. I've run it on jizo as well as my >>>> home >>>> machine with the same error. >>>> >>>> >>>> Cut-and-paste the following info into your FreeSurfer problem report: >>>> --------------------------------------------------------------------- >>>> >>>> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 >>>> >>>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >>>> >>>> RedHat release: CentOS release 6.4 (Final) >>>> >>>> Kernel info: Linux 2.6.32-358.2.1.el6.x86_64 x86_64 >>>> >>>> NMR Center info (/space/freesurfer exists): >>>> >>>> machine: jizo >>>> >>>> SUBJECTS_DIR: /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs >>>> >>>> PWD: /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs >>>> >>>> ssh jizo >>>> setenv SUBJECTS_DIR >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs >>>> cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs >>>> --------------------------------------------------------------------- >>>> >>>> I would appreciate any help. Let me know if anything is unclear. >>>> >>>> Thank! >>>> Best, >>>> Omar >>>> >>>> Error Message >>>> ************* >>>> >>>> [jizo:fc_fs] (nmr-stable53-env) fcseed-sess -s AC30_1319 -cfg >>>> vcsf_bold1_config -overwrite >>>> Logfile is >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/log/fcseed-sess.vcsf_bold1_config.log.AC30_1319 >>>> Wed Aug 14 11:31:50 EDT 2013 >>>> Linux jizo 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC >>>> 2013 >>>> x86_64 x86_64 x86_64 GNU/Linux >>>> setenv SUBJECTS_DIR >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs >>>> cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs >>>> /usr/local/freesurfer/stable5_3_0/fsfast/bin/fcseed-sess >>>> -s AC30_1319 -cfg vcsf_bold1_config -overwrite >>>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >>>> Wed Aug 14 11:31:50 EDT 2013 >>>> Linux jizo 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC >>>> 2013 >>>> x86_64 x86_64 x86_64 GNU/Linux >>>> setenv SUBJECTS_DIR >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs >>>> cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs >>>> /usr/local/freesurfer/stable5_3_0/fsfast/bin/fcseed-sess >>>> -s AC30_1319 -cfg vcsf_bold1_config -overwrite >>>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >>>> >>>> mri_label2vol --seg >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/mri/aparc+aseg.mgz >>>> --reg >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/register.dof6.dat >>>> --temp >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/template.nii.gz >>>> --fillthresh .95 --o >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz >>>> --pvf >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/pvf.nii.gz >>>> PVF >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/pvf.nii.gz >>>> Number of labels: 0 >>>> Annot File: (null) >>>> Template Volume: >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/template.nii.gz >>>> Outut Volume: >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz >>>> Registration File: >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/register.dof6.dat >>>> Fill Threshold: 0.95 >>>> Label Vox Vol: 1 >>>> ProjType: (null) >>>> ProjTypeId: 0 >>>> ProjStart: 0 >>>> ProjStop: 0 >>>> ProjDelta: 0.1 >>>> Subject: (null) >>>> Hemi: (null) >>>> UseNewASeg2Vol: 1 >>>> DoLabelStatVol 0 >>>> LabelCodeOffset 0 >>>> setenv SUBJECTS_DIR >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs >>>> $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ >>>> Template RAS-to-Vox: -------- >>>> -0.320 0.000 0.000 32.000; >>>> -0.000 -0.000 -0.320 32.000; >>>> -0.000 0.167 -0.000 12.500; >>>> 0.000 0.000 0.000 1.000; >>>> Template Voxel Volume: 58.5938 >>>> nHits Thresh: 55.6641 >>>> Loading registration from >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/register.dof6.dat >>>> RegMat: -------- >>>> -0.106 0.977 -0.185 7.376; >>>> -0.994 -0.104 0.019 -0.687; >>>> -0.000 0.186 0.983 -23.526; >>>> 0.000 0.000 0.000 1.000; >>>> Label RAS-to-Vox: -------- >>>> 0.034 -0.313 0.059 29.640; >>>> 0.000 -0.059 -0.314 39.528; >>>> -0.166 -0.017 0.003 12.385; >>>> 0.000 0.000 0.000 1.000; >>>> ASeg2Vol: Building LUT >>>> ASeg2Vol: Sorting >>>> ASeg2Vol: Mapping >>>> ASeg2Vol: Reverse Map >>>> nmisses = 1120 (0 filled) >>>> ASeg2Vol: done >>>> PVF >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/pvf.nii.gz >>>> Computing PVF 58.5938 >>>> mri_binarize --i >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz >>>> --o >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz >>>> --match 4 --match 5 --match 43 --match 44 --match 31 --match 63 >>>> >>>> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ >>>> cwd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs >>>> cmdline mri_binarize --i >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz >>>> --o >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz >>>> --match 4 --match 5 --match 43 --match 44 --match 31 --match 63 >>>> sysname Linux >>>> hostname jizo >>>> machine x86_64 >>>> user osinglet >>>> >>>> input >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz >>>> frame 0 >>>> nErode3d 0 >>>> nErode2d 0 >>>> output >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz >>>> Binarizing based on matching values >>>> nMatch 6 >>>> 0 4 >>>> 1 5 >>>> 2 43 >>>> 3 44 >>>> 4 31 >>>> 5 63 >>>> binval 1 >>>> binvalnot 0 >>>> Found 0 values in range >>>> Counting number of voxels >>>> Found 0 voxels in final mask >>>> mri_binarize done >>>> mri_segstats --i >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/fmcpr.nii.gz >>>> --seg >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz >>>> --id 1 --sum >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/junk.sum >>>> --avgwfvol >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/avgwf.mgh >>>> >>>> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ >>>> cwd >>>> cmdline mri_segstats --i >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/fmcpr.nii.gz >>>> --seg >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz >>>> --id 1 --sum >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/junk.sum >>>> --avgwfvol >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/avgwf.mgh >>>> sysname Linux >>>> hostname jizo >>>> machine x86_64 >>>> user osinglet >>>> UseRobust 0 >>>> Loading >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz >>>> Loading >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/fmcpr.nii.gz >>>> Voxel Volume is 58.5938 mm^3 >>>> Generating list of segmentation ids >>>> Found 1 segmentations >>>> Computing statistics for each segmentation >>>> 0 1 0 0.000 >>>> MRIalloc(0, 1, 1): bad parm >>>> >>>> Reporting on 0 segmentations >>>> Computing spatial average of each frame >>>> >>>> Writing to >>>> /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/avgwf.mgh >>>> Segmentation fault (core dumped) >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > >

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Different results related to ICV (eTIV) difference between FS 4.5.0 and 5.3.0 - any suggestions?
by Kjetil Nordbø Jørgensen 24 Aug '13

24 Aug '13

Dear FreeSurfer experts! I have a problem which relates to the ICV (eTIV) measure in different versions, and would be thankful for any suggestions: I have previously examined associations between body mass index (BMI) and global cortical measures (e.g. cortical volume) in a sample of patients with severe mental illness using stats from FS 4.5.0. I then found a small but significant positive association between BMI and volume (p<0.05) (corrected for age, gender and diagnosis), which became more highly significant when covarying for ICV (p<0.0001). According to my hypothesis, I interpreted this as a tendency towards larger brains relative to skull size with increasing BMI (it should be noted that although the association was significant, a beta-value of about .1 indicated the effect was small). Now, when I updated the analyses with stats from FS 5.3.0, using the same data set, no significant results emerge: The positive association is now at trend-level (p=0.105), and when covarying for ICV (eTIV) it disappears altogether. I’m struggling to understand this difference. The analyses are fairly similar up to the point where ICV (eTIV) is added as a covariate, but adjusting for ICV changes the results quite a lot. Both cortical volume and ICV correlates highly between the two versions (r = .96 and .94, respectively), but when I calculate cortical volume/ICV-ratios based on stats from each version, the correlation between these is lower (r = .75). I have so far ruled out (I believe) any differences in quality control or editing as a source of the difference. Both versions have used the talairach.xfm transform and not the older talairach_with_skull. The problem could be related to collinearity (correlations between cortical volume and ICV were r=.81 in FS 4.5.0 and r=.74 in FS 5.3.0), but VIF and tolerance statistics does not indicate a problem (and I suppose this would affect results equally much between versions (?)). So, my questions are: - Are there any differences between FS 4.5.0 and FS 5.3.0 in how ICV (eTIV) is calculated? - Is it inappropriate to correct for intracranial volume when examining global cortical volume rather than regional volumes? - Do any of you have suggestions as to how I can figure out what is the ‘true’ result here? Any help is appreciated!

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