Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

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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ICV meaning...
by Gonzalo Rojas 28 Apr '10

28 Apr '10

Hi: Which is the meaning of the Intracaranial Volume (ICV) ?... it includes only the brain, or also the skull ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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ICV meaning...
by Gonzalo Rojas 28 Apr '10

28 Apr '10

Hi: In aseg.stats file, appears "lh-cerebral-white-matter" and "Left-Cerebral-White-matter": which are the difference between both values?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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converting label to binary mask.mgh
by Ritobrato Datta 28 Apr '10

28 Apr '10

Hello All, I have created a V1 label using Hinds and Fischl Method. Is a label a .mgh file as well ?? How do I convert this label to a binary mask mgh file ? Please let me know. Thanks much Rito

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Question about cortical surface area
by Massieh Moayedi 28 Apr '10

28 Apr '10

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

2 1

Group comparison -qdec clarification
by Rajagopalan, Venkateswaran 28 Apr '10

28 Apr '10

Dear All, I want to perform group comparison of cortical thickness between my patient and control group. I read qdec tutorial regarding how to do this. I was little bit puzzled and not able to understand the following. Before creating qdec table of patient data, fsaverage was suggested to run, so that the data will be resampled and smoothed. If i understand correctly this is to have all the data in the same space so that we can perform statistical tests on them I am new to freesurfer and entire processing steps. Also I would like to know if patient data is resampled and smoothed using fsaverage then my files in stats folder namely aparac.stats will have values little bit different from the ones after the recon-all -all step am i right. One other question i have 4 different patients groups so for instance if i want to compare whether group 1 >group 2 then my contrast will be 1 -1, if also want to check whether group 2>group1 then my contrast will be -1 1 am I right. Thanks in advance venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by 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 the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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