Freesurfer February 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
126 discussions

FreeSurfer Tutorial and Workshop in Sao Paulo, Brazil
by Pedro Paulo de Magalhães Oliveira Junior 16 Feb '09

16 Feb '09

The FreeSurfer <http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> Development Team is hosting a two-day course for beginner and experienced users of FreeSurfer <http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer>. Day 1 will be an introduction toFreeSurfer<http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> (or a refresher for those more experienced). Day 2 will cover everything you need to know for analyzing your data. Topics are listed below. There are only *30 available spots* for this course. The course will not cover FS-FAST neither fMRI analysis. Computers will be provided to all pairs of registrants, which will have FreeSurfer <http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> and data already installed. Attendees will work in pairs (sharing a computer). The course will be held at Sao Paulo health care complex of HCFMUSP. The lecturers will be: Nick Schmansky, Allison Stevens and Lilla Zollei For more information: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/BrazilCourseSchedule For requesting a place in the course please write to my e-mail. I think it's a great opportunity for people from Latin America and South Africa. Best Regards, Pedro Paulo Oliveira Jr ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom

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cortical thickness in temporal pole
by Lucia Garrido 16 Feb '09

16 Feb '09

Dear all, I'm comparing average cortical thickness values between groups using regions defined in the aparc files. I find significant differences in the right temporal pole. I was expecting difference here, but I'm concerned about the mean values of thickness. For controls, that value is 4.01, whereas in the left temporal pole is 3.80. Could anyone let me know if these values look too high? Thank you very much. best wishes, lucia

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About left-right hemisphere interpretations
by Francisco Robles 13 Feb '09

13 Feb '09

Hello free Surfer communities, I'm Francisco Robles from the Instituto Nacional de Neurología y Neurocirugía in México City and I habe a serious boubt about Free Surfer Analysis, is a basic one son I am kind of embarrased to ask it but is realllly important. I really do not know if left hemisphere activation is the left one and right is really the right activation one in FS-FAST. I got my images from a GE MRI in dicom in a radiological view (left is right and viceversa) and converted it to analyze in MRI-Converter. Then I gave the analyze images the hole FreeSurfer Processing with strcutural and the same for FS-FAST. I never changed the images, so I guess left stands as right and right stands as left except if FS-FAST knows it was a radiological view and changed it. My doubt comes now because the regions significantly activated according to FS-FAST seem to contradict what I expected. Thank you all in advance and thanks for putting this invaluable instrument for free and the techinical support also. _________________________________________________________________ Sabes que son imágenes dinámicas en Messenger? Descúbrelo. http://download.live.com/messenger

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(no subject)
by Keller, Corey J. 13 Feb '09

13 Feb '09

Hi Freesurfers, We have an MRI coregistered with a CT scan using spmregister. I have converted the CT to the anatomical volume using mri_vol2vol. We are then trying to view the anatomical ct in tkmedit and output talairach coordinates but as of now can only see RAS coordinates. Is there a way to either view the talairach coordinates or to transform the RAS to talairach coordinates? The former would be ideal. tkmedit -SUBJECT ct.anat.nii lh.pial Thanks. Best, Corey

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Re: [Freesurfer] new eTIV calculation
by bell0368＠umn.edu 13 Feb '09

13 Feb '09

Nick, Just a clarification question. I read the wiki regarding the new eTIV and it says that the registration to $FREESURFER_HOME/average/711-2C_as_mni_average_305.4dfp.img is done with talairach_avi as opposed to imgreg_4dfp. I am guessing imgreg_4dfp is correct because the template has 4dfp right in its name. Also, I have not used imgreg_4dfp before, and looking at its options I was curious what a t4file and mode were; two of its listed options. Does this command generate a .xfm file? Thanks. Chris

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Qdec question
by Devdutta W 13 Feb '09

13 Feb '09

Hi, I have been running into an error while using Qdec. *Error in Analyze: Couldn't open file <$SUBJECT_DIR>/<SUBJECT_FOLDER>/surf/lh.thickness.fwhm10.fsaverage.mgh* I checked and the file is there in that folder. I know this file is created when recon-all is run with -qcache option. I have run that twice and it still gives me the same error. What could be going wrong here and how can I fix it? Thanks, Dev

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Cannot allocate memory
by Jürgen Hänggi 13 Feb '09

13 Feb '09

Dear FS experts I tried to make an average subject of 52 subjects, but it seems that an already fixed error is back: Checking 47 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po laris_Male_48.mgh Checking 48 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po laris_Male_49.mgh Checking 49 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po laris_Male_50.mgh Checking 50 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po laris_Male_51.mgh Checking 51 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po laris_Male_52.mgh nframestot = 52 Allocing output MRIalloc(256, 256, 256): could not allocate 262144 bytes for 11862th slice Cannot allocate memory ERROR: make_average_volume [Neuropsycho@130 subjects]$ I had the same problem with an older Mac FS version. Is there also a fixed version of FS 4.2.0 for Linux CENTOS 32 bit? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division 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[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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eTIV
by Gabriel Go.Es. 13 Feb '09

13 Feb '09

Dear freesurfers: I have two questions: 1. I have FS v4.0.5 and i've downloaded the new mri_segstats to calculate the eTIV, this new calculation may cause any trouble in my group of manual segmented subjects? 2. I have 60 subjects manual segmentated on FreeSrufer 4.0.5, i want to know if i run the recon2 or recon3 in the new FS 4.2.0, will have any problem? the diferences between versions can cause any trouble with the analisis because imcompability or something? Regards Gabriel ¿Tu fondo de escritorio es aburrido? Anímalo con las imágenes más espectaculares _________________________________________________________________ Consigue gratis el nuevo Messenger. ¡Descárgatelo! http://download.live.com/

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13 Feb '09

Dear all, I would like to automatically corregister PET to MRI by using the command bbregister. I am not sure what is going on since Freesurfer (release 4.0.5) always says "Command not found" when I try to run this function. Any help with this issue would be very welcome. 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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new eTIV calculation
by Nick Schmansky 13 Feb '09

13 Feb '09

If you make use of the estimated Total Intracranial Volume (eTIV) calculation found in the aseg.stats file of your subject data, then you should be aware that we have recently found a more accurate way to make this calculation. We have found that using the talairach.xfm transform instead of the talairach_with_skull.lta transform, from which the determinant is extracted and multiplied by a scale factor, results in lower variability of the eTIV calc in our test set. This new way of calculating eTIV will appear in the next release of Freesurfer. If you want to make use of this new calculation right away, you can download a new version of mri_segstats from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes and run it using this command: mri_segstats --subject subjid --etiv-only and it will output the new eTIV. Nick

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Freesurfer February 2009