Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Correction
by Juergen Haenggi 20 Mar '07

20 Mar '07

Dear Freesurfer users In my former email, I meant that I can not change from bash to tcsh shell on Mac OS X. Sorry! Thanks Regards Juergen --------------------------------------------------------------------------- Juergen Haenggi, Ph.D. student Department of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ---------------------------------------------------------------------------

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RE: [Freesurfer] RE: Version compatability
by Fornito, Alexander 19 Mar '07

19 Mar '07

Hi Nick, One thing I couldn't work out from the example image associated with the release notes is whether the different areas are located in the non-cortical regions of the midline. If they include cortical regions (and it appears that subgenual portions of the cingulate are) then I am interested in these areas. Ta, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito(a)wh.org.au

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Legacy flag
by Fornito, Alexander 19 Mar '07

19 Mar '07

Hi, I was just seeking some clarification re: the legacy flag in recon-all. Can I use it on subjects procssed with older versions of Freesurfer to reconstruct surfaces that will be consistent with those generated with older versions (i.e., I can collapse data from the two versions), or is the legacy flag intended to allow new versions of recon-all to be used on old data, effectively 'updating' the surfaces (meaning they should not be analyzed together with data generated using older versions). Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito(a)wh.org.au

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getting info from recon-all.log
by Sameer Walawalkar 16 Mar '07

16 Mar '07

Hello, My recon-all command (actually two of them) ran for some 30 hrs and 12 hours (the second one with nohup) before my windows macine rebooted. I wanted to see what was the status of the imlementation and so decided to look into the Status and Log Files. Both recon-all.log and recon-all-status.log files have the same entry given below. MNE software location set to /mnt/data/home/sameer/Software/MEGswdir/mne MATLAB software location set to /mnt/data/home/sameer/Software/MEGswdir/matl ab /mnt/data/home/sameer/Software/MEGswdir/mne/bin/mne already in PATH Note : Remember to set SUBJECTS_DIR and SUBJECT environment variables correctly. Note : FreeSurfer environment is needed to run mne_setup_source_space This really doesn't tell me anything. Can someone please shed some light on this? thanks, sameer

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Announcement: open access MR data (OASIS)
by Daniel Marcus 15 Mar '07

15 Mar '07

Dear Colleagues, The Open Access Series of Imaging Studies (OASIS) is now available at www.oasis-brains.org <http://www.oasis-brains.org/> . The data are publicly available under to a liberal Data Use Agreement available here: http://www.oasis-brains.org/app/template/UsageAgreement.vm. The first data set includes structural MR obtained from 416 subjects aged 18 to 96, including 100 subjects diagnosed with very mild to moderate Alzheimer's Disease. A longitudinal data set will be released in the coming months. A manuscript describing the project is currently in press at Journal of Cognitive Neuroscience. For more information, please visit the website. Of particular interest to this group, Bruce Fischl's group is kindly churning the whole data set through Freesurfer. The resulting goodies will be made freely available as open access data. Make sure to thank Bruce and Jenni next time you see them. Regards, Dan Marcus dmarcus(a)wustl.edu Neuroinformatics Research Group Washington University School of Medicine http://nrg.wustl.edu <http://nrg.wustl.edu/>

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importing cartesian coordinates file
by abel cruz vadell 14 Mar '07

14 Mar '07

Hi everyone Could I import in FreeSurfer (specifically in TKSurfer) a cartesian coordinates files? I need to locate the position of my EEG electrodes (previously translated to the brain and each one containing the information of one hemisphere) into the surfaces generated in FreeSurfer (orig and inflated). Is there any registration tool in FreeSurfer to do that? Or any other way? Thanks ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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mri_convert and recon-all
by Sameer Walawalkar 14 Mar '07

14 Mar '07

Hello, I have two questions. 1> I am following instructions from http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-platform-releas… Under GETTING STARTED WITH YOUR OWN DATA there are two directives: cp -r <path_to_dicoms>/95555-2-*.dcm 001/ cp -r <path_to_dicoms>/95555-3-*.dcm 002/ with special note: . Note that in your own case, the name of the dicom files will be different (in this example, 95555-2-*.dcm consisted of 128 files). My MRI data is essentially a directory (directory name is a many digit number like 123456789) with four subdirectories named 1, 2, 3 and 4. So I have used the following commands cp -r <path_to_dicoms>/12345..../1/*.dcm 001/ cp -r <path_to_dicoms>/12345.../2/.dcm 002/ This is because directories 2 and 3 have 256 slices whereas 1 and 4 had six slices. (this could change from subject to subject) After that I do mri_convert -it dicom -ot mgz 001/ 001.mgz mri_convert -it dicom -ot mgz 002/ 002.mgz Is this correct procedure? This does create the .mgz files. 2> After this, I gave the command recon-all -autorecon-all -subjid <subjid> and this has been running for many hours now (as warned on the website). It has already created slices and sets. My understanding is it will do just about everything INCLUDING triangulation which is used for BEM forward moderls using MNE. Is this correct? Thanks for your help. best, sameer

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how to deal with the cortex surface?
by duhanjian 14 Mar '07

14 Mar '07

hi ,I don't how to render the surface from A picture to B picture in SUMA? look carefully,the cortex surface is different,and I want to B effect.so does anyone has idea to deal with it?Thank you! 本邮件附件清单如下： (1) A picture.JPG (26.6 K) (2) B picture.JPG (26.8 K) duhanjian，duhanjian(a)sohu.com 2007-03-15

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MGZ image format
by nayoung＠cis.jhu.edu 14 Mar '07

14 Mar '07

I put in my 161 x 191 x 151 Analyze image into Freesurfer and get 256 x 256 x 256 MGZ image. I need to make the scan back to my original .img format with original image size. I ran mri_convert and it gives me an image size of 256 x 256 x 256 or I tried -like option and it interpolates the data which I do not want. Thank you. Nayoung

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use modified annotation file for parcellation
by Leila BH 13 Mar '07

13 Mar '07

Hello, I modified the annotation file rh.aparc.annot to 'rh.myaparc.annot' I can read it with read_annotation.m and it seems correct. (The modification is simply a subdivision of the middletemporal to 32 subregion named : middletemporal_1 .middletemporal_32). I copied this 'rh.myaparc.annot' file to /usr/local/freesurfer/sibjects/fsaverage/label/rh.myaparc.annot (I did this because the original 'rh.aparc.annot' file was there. When I run the mris_ca_label as done in the log file generated by recon-all command: mris_ca_label chuv44 rh ../surf/rh.sphere.reg /usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot ../label/rh.myaparc.annot I have an error: GCSAread(/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot): file magic #28002 != GCSA_MAGIC (ababcdcd) mris_ca_label: could not read classifier from /usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot How can I do to use this annotation file? Is it necessary to have GCS file for parcellation? If yes how can I create it with this annotation file. I don't want to create my own atlas, I want to use the freesurfer atlas (35 entries) but just divide some of its regions. If needed, I can send you my annotation file. Thanks a lot

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