Freesurfer April 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
147 discussions

MRS mask
by Lena Palaniyappan 12 May '10

12 May '10

Hi Bruce and team I have a ROI mask in analyze (img_hdr) format obtained from MR spectroscopic group analysis using a different registration (talairach based). I want to use this ROI as a label to extract thickness measures on a group of subjects. How can I do this? If I use mri_vol2surf will I be not projecting contrasts from a differently registered image set onto reconstructed freesurfer anatomical? Cheers 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.

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cortical thickness calculation
by miro drahos 30 Apr '10

30 Apr '10

Dear Surferteam, I have been trying to understand details on how the cortical thickness is calculated. I read in the article: "we compute the closest vertex on the pial from each vertex on the white, and vice-versa, then set the thickness to the average of the two." I have tried to carry out this calculation myself, using the generated surfaces lh.white and lh.pial and compare my results to the thickness generated by FS (lh.thickness). There is a one-to-one correspondence between the vertices of the white and pial meshes, which makes it quite straightforward: e.g.: Vertex 100 on white surface has distance from pial surface = 2.5 mm, vertex 100 on pial surface has distance from white surface = 2.6 mm, average == thickness at vertex 100 = 2.55 mm. However, the results that I am getting are different from lh.thickness. I expected discrepancies on the order of rounding errors, but half of the thickness values differ more than 0.001, with some differing as much as 2 mms! What am I missing? Could you please elaborate a bit on how you define the cortical thickness? Thank you very much, Miro Drahos

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Re: [Freesurfer] nu-correct parameters
by Nick Schmansky 30 Apr '10

30 Apr '10

as long as the special parameters for nu_correct are the last ones in the parameter string, after the -all flag. On Fri, 2010-04-30 at 10:45 +0200, Leonardo Chesi wrote: > Hi Nick, > > tank a lot for your help. I’ve tried to launch the segmentation as you > had write me but I received back some errors. So I have try to add to > the command line the –autorecon-all parameters because it try to find > some volumes that there wasn’t in that folder. With the –autorecon-all > parameters the segmentation is started and I’m waiting for the results > that I can see when I come back to work on Monday. I hope that adding > the –autorecon-all parameters is all ok. I wait for your courteous > reply for that parameters. If you need more information about the > error I can send you on Monday the terminal window. > > hoping that my mail has not bothered you, and thank you for the help, > sincerely > > Leonardo > >

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Re: [Freesurfer] nu-correct parameters
by Leonardo Chesi 30 Apr '10

30 Apr '10

Hi Nick, tank a lot for your help. I've tried to launch the segmentation as you had write me but I received back some errors. So I have try to add to the command line the -autorecon-all parameters because it try to find some volumes that there wasn't in that folder. With the -autorecon-all parameters the segmentation is started and I'm waiting for the results that I can see when I come back to work on Monday. I hope that adding the -autorecon-all parameters is all ok. I wait for your courteous reply for that parameters. If you need more information about the error I can send you on Monday the terminal window. hoping that my mail has not bothered you, and thank you for the help, sincerely Leonardo

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FMRI values at surface vertices?
by Dickinson, Annelise (NIH/NIMH) [F] 29 Apr '10

29 Apr '10

Hi all, Sorry if this is a dumb question-is there any way to create a Matlab-readable (e.g. Text) file containing the fMRI values at each surface vertex of a painted surface? Please let me know if you have any idea! Thank you so much, Elise ***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona(a)mail.nih.gov

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How to find out which package of FSL is used by FreeSurfer
by Ed Gronenschild 29 Apr '10

29 Apr '10

Hi, The FreeSurfer package is bundled with a subset of FSL. However, I think most of us also installed the full FSL package. The global variable FSL_DIR points to the directory of FSL. My question is if it is possible to read from recon-all log files which FSL package is used? Ed

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converting dicom files into mgz, looking forward to some help, thank you!
by 昌明 29 Apr '10

29 Apr '10

Dear Freesurfers: i failed every time i tried to transform my dicom GE structrual images into mgz format, because i am quite new for this software, so i'd like to ask some help from you. i will be very grateful if you can tell me what the reason is, or give me some suggestions on how to fix the problem. my command lines and the error messages are as below. thank you very much! changming [chenchangmingswu@localhost ~]$ cd /media/12D8F3B3D8F392E9/chenchangming/20071119/csq [chenchangmingswu@localhost csq]$ cd . [chenchangmingswu@localhost csq]$ ls 0001.dcm 0023.dcm 0045.dcm 0067.dcm 0089.dcm 0111.dcm 0133.dcm 0155.dcm 0002.dcm 0024.dcm 0046.dcm 0068.dcm 0090.dcm 0112.dcm 0134.dcm 0156.dcm 0003.dcm 0025.dcm 0047.dcm 0069.dcm 0091.dcm 0113.dcm 0135.dcm 0157.dcm 0004.dcm 0026.dcm 0048.dcm 0070.dcm 0092.dcm 0114.dcm 0136.dcm 0158.dcm 0005.dcm 0027.dcm 0049.dcm 0071.dcm 0093.dcm 0115.dcm 0137.dcm 0159.dcm 0006.dcm 0028.dcm 0050.dcm 0072.dcm 0094.dcm 0116.dcm 0138.dcm 0160.dcm 0007.dcm 0029.dcm 0051.dcm 0073.dcm 0095.dcm 0117.dcm 0139.dcm 0161.dcm 0008.dcm 0030.dcm 0052.dcm 0074.dcm 0096.dcm 0118.dcm 0140.dcm 0162.dcm 0009.dcm 0031.dcm 0053.dcm 0075.dcm 0097.dcm 0119.dcm 0141.dcm 0163.dcm 0010.dcm 0032.dcm 0054.dcm 0076.dcm 0098.dcm 0120.dcm 0142.dcm 0164.dcm 0011.dcm 0033.dcm 0055.dcm 0077.dcm 0099.dcm 0121.dcm 0143.dcm 0165.dcm 0012.dcm 0034.dcm 0056.dcm 0078.dcm 0100.dcm 0122.dcm 0144.dcm 0166.dcm 0013.dcm 0035.dcm 0057.dcm 0079.dcm 0101.dcm 0123.dcm 0145.dcm 0167.dcm 0014.dcm 0036.dcm 0058.dcm 0080.dcm 0102.dcm 0124.dcm 0146.dcm 0168.dcm 0015.dcm 0037.dcm 0059.dcm 0081.dcm 0103.dcm 0125.dcm 0147.dcm 0169.dcm 0016.dcm 0038.dcm 0060.dcm 0082.dcm 0104.dcm 0126.dcm 0148.dcm 0170.dcm 0017.dcm 0039.dcm 0061.dcm 0083.dcm 0105.dcm 0127.dcm 0149.dcm 0171.dcm 0018.dcm 0040.dcm 0062.dcm 0084.dcm 0106.dcm 0128.dcm 0150.dcm 0172.dcm 0019.dcm 0041.dcm 0063.dcm 0085.dcm 0107.dcm 0129.dcm 0151.dcm 0020.dcm 0042.dcm 0064.dcm 0086.dcm 0108.dcm 0130.dcm 0152.dcm 0021.dcm 0043.dcm 0065.dcm 0087.dcm 0109.dcm 0131.dcm 0153.dcm 0022.dcm 0044.dcm 0066.dcm 0088.dcm 0110.dcm 0132.dcm 0154.dcm [chenchangmingswu@localhost ~]$ unpacksdcmdir -scanonly scan.dat -src . -targ . $Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $ /home/chenchangmingswu -scanonly scan.dat -src . -targ . Thu Apr 29 07:05:51 EDT 2010 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/29-11:05:51-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ User: chenchangmingswu Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.31.5-127.fc12.i686.PAE CompilerName: GCC CompilerVersion: 30400 localhost.localdomain Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7 21:25:57 EST 2009 i686 athlon i386 GNU/Linux Thu Apr 29 07:05:51 EDT 2010 Log File is ./unpack.log INFO: Logfile is ./unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is ./dicomdir.sumfile INFO: status file is ./parse.status Scanning directory Thu Apr 29 07:05:51 EDT 2010 mri_parse_sdcmdir --sortbyrun --d . --o ./dicomdir.sumfile --status ./parse.status 0 Done scanning Thu Apr 29 07:05:51 EDT 2010 ------------------------------------------ ERROR: no dicom files found in . [chenchangmingswu@localhost csq]$ recon-all -force -i /media/12D8F3B3D8F392E9/chenchangming/20071119/csq -subjid csq INFO: /media/12D8F3B3D8F392E9/chenchangming/fs-analysis/csq exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /media/12D8F3B3D8F392E9/chenchangming/fs-analysis Actual FREESURFER_HOME /home/chenchangmingswu/software/freesurfer -rwxrwxrwx. 1 chenchangmingswu chenchangmingswu 15854 Apr 28 12:46 /media/12D8F3B3D8F392E9/chenchangming/fs-analysis/csq/scripts/recon-all.log Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7 21:25:57 EST 2009 i686 athlon i386 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /home/chenchangmingswu/software/freesurfer/ Previous: /home/chenchangmingswu/software/freesurfer /media/12D8F3B3D8F392E9/chenchangming/fs-analysis/csq mri_convert /media/12D8F3B3D8F392E9/chenchangming/20071119/csq /media/12D8F3B3D8F392E9/chenchangming/fs-analysis/csq/mri/orig/001.mgz mri_convert /media/12D8F3B3D8F392E9/chenchangming/20071119/csq /media/12D8F3B3D8F392E9/chenchangming/fs-analysis/csq/mri/orig/001.mgz corRead(): can't open file /media/12D8F3B3D8F392E9/chenchangming/20071119/csq/COR-.info $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /media/12D8F3B3D8F392E9/chenchangming/20071119/csq... Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7 21:25:57 EST 2009 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Thu Apr 29 07:53:34 EDT 2010

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Re: [Freesurfer] Question about cortical surface area
by j janssen 29 Apr '10

29 Apr '10

Hi, what's the reason that FS's default surface for measuring surface area is the white matter surface and not the pial surface? why isn't surface area measured on the intermediate surface (average of gray.and white which should be less biased by sulci and gyri, i think)? thanks, -joost > > > On Wed, Apr 28, 2010 at 5:48 PM, Michael Harms > > <mharms(a)conte.wustl.edu> wrote: > > > > Hi Massieh, > > There were some posts related to this a while back. > > If I recall correctly, the vertex-wise area measure (and > > likewise the > > vertex-wise volume measure) is highly dependent on the local > > mesh > > triangulation, and thus is not really a meaningful variable > > from a > > biological perspective. So, you would be better off analyzing > > the area > > of a whole label. > > > > Best, > > -Mike H. > > > > > > > > On Wed, 2010-04-28 at 09:54 -0400, Massieh Moayedi wrote: > > > Hi everyone, > > > > > > I had two questions: > > > > > > 1) I was wondering if it's ok to run a glm to compare > > cortical surface > > > areas between two groups on a vertex-wide basis (just like a > > thickness > > > analysis). Or is it better to extract the area of a label > > (as is the > > > output of mri_anatomical_stats)? > > > > > > 2) The mri_anatomical_stats output includes 4 measures of > > curvature: > > > MeanCurv, GausCurv, Van Essen Folding index and Curvature > > Index. There > > > was some discussion as to which of these was most > > appropriate for > > > comparing sulcal folding (that is, essentially what they > > measure, > > > correct?)- was there ever any final consensus? > > > > > > Thank you. > > > > > > Regards, > > > > > > Massieh Moayedi B.Sc. (Hons) > > > PhD Student > > > Dr. Karen Davis' Lab > > > Institute of Medical Science > > > University of Toronto > > > > > > Brain, Imaging and Behaviour- Systems Neuroscience > > > MP 14-301 > > > Toronto Western Research Institute > > > University Health Network > > > 399 Bathurst Street > > > Toronto, Ontario > > > Canada M5T 2S8 > > > Tel: 416-603-5882 > > > > > > massih.moayedi(a)utoronto.ca > > > mmoayedi(a)uhnres.utoronto.ca > > > http://individual.utoronto.ca/PSMJC > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the > > person to whom it is > > > addressed. If you believe this e-mail was sent to you in > > error and the e-mail > > > contains patient information, please contact the Partners > > Compliance HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was > > sent to you in error > > > but does not contain patient information, please contact the > > sender and properly > > > dispose of the e-mail. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >

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GM/WM volumes
by Jory Hoogendam 29 Apr '10

29 Apr '10

Hello Freesurfer experts, Sorry for the repost, but I'm still hoping someone can answer our questions found below. We have generated a list of volumes, using asegstats2table (based on aseg.stats files). We want to compute total grey matter (including subcortical GM) and white matter volumes for right and left hemispheres, separately for the cerebebrum and cerebellum. Which volumes from the list should we sum to generate these grey matter and white matter volumes? Further, which volumes should be included to calculate CSF for the whole brain? Thanks in advance, Jory Hoogendam

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error while unzipping SuSE Itanium release
by Amir Tahmasebi 28 Apr '10

28 Apr '10

Hi there, I am getting the following error when unzipping the SuSE Itanium release: "tar: Archive contains obsolescent base-64 headers" Any help is appreciated. Thank you in advance, Regards, Amir -- ________________________________ Amir M. Tahmasebi, Ph.D. Medical Image Analysis Lab. School of Computing, Queen's University, Kingston, Ontario CANADA K7L 3N6 ________________________________ Tel: (613) 533-2797 Web: www.cs.queensu.ca/~tahmaseb

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Freesurfer April 2010