Freesurfer

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30132 discussions

MEF segmentation: FLASH_atlas.gca
by Auer, Tibor MD. Ph.D. 06 Jun '11

06 Jun '11

Dear Freesurferers, I am trying to process multi-echo FLASH (MEF) images with FS. I have read in FSWiki, that the FLASH_atlas.gca was built precisely for MEF data acquired with FA=5 and FA=30. However, when I have looked after FLASH_atlas.gca in the FS installation, I have found none. Is it possible to obtain it somehow? Thanks, Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Mobile: +49-(0)176-8012-7921 E-Mail: tauer(a)gwdg.de <mailto:tibor.auer@gmail.com>

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cerebellum atlas template
by Anthony Dick 06 Jun '11

06 Jun '11

I didn't get a response the last post, so I'm going to try one more time! Hello all, We are looking to develop a cerebellum atlas training set based on the Schmahmann et al (2000) parcellation so we can automatically segment the cerebellum based on this atlas. Does this exist already? I know Makris and colleagues had done something similar to this, but I am not sure if it has been developed for Freesurfer. Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://www.fiu.edu/~adick

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Q: Talairach Transformation
by Yiyu Chou 06 Jun '11

06 Jun '11

Dear Freesufer Users: I wonder if the Talairach transformation engine was modified on version 5.1 or not, since I got an error message that didn't happen with version 5.0 on the same subject when running recon-all: "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***" I would appreciate it if you can give me some advice. Yi-Yu Chou

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Job advertisement! - Munich, Germany
by Direktion, Institut f. Schlaganfall- und Demenzforschung 06 Jun '11

06 Jun '11

The Hospital of the University of Munich, Germany, is one of the largest and most competitive university hospitals in Germany and Europe. 45 specialized hospitals, departments and institutions harbouring excellent research and education provide patient care at the highest medical level with approximately 10.000 employees. The Institute for Stroke and Dementia Research (ISD) is a newly founded institution financed from foundation funds. The activity ranges from basic research to clinical trials (www.isd-muc.de<file:///C:\Dokumente%20und%20Einstellungen\mfruehau\Lokale%20Einstellungen\Temporary%20Internet%20Files\Content.Outlook\RDUQYX6B\www.isd-muc.de>). After completion of the construction phase, the Institute for Stroke and Dementia research will employ around 100 staff members, graduate students, scholars and foreign scholars. The Institute for Stroke and Dementia Research (ISD) is looking at the earliest opportunity for a *Research Associate in MR imaging* RESPONSIBILITIES: We are looking for a motivated scientist with methodological expertise in MR imaging and good programming skills (e.g. C, C ++, Pearl, Python, Scripting Languages, Matlab). Knowledge about data collection, processing and analysis of functional and structural MR imaging data and an interest in neuro-scientific questions are desired. REQUIREMENTS: University degree. OFFER: Our Institute offers an excellent multidisciplinary environment (medical scientists, neuropsychologists, biologists, bioinformaticians, epidemiologists) with modern IT infrastructure and use of human MR scanners (1.5T and 3T). A new building with its own small-animal-imaging equipment (micro-PET and -MRI) is currently being built (www.isd-muc.de) The tasks include the establishment of new analytical methods for MRI-data, participation in ongoing research projects, and development of own project ideas. Salary is according to TV-L. The position is limited for two years, but extension is desired. Disabled persons will be preferentially considered in case of equal qualification. Presentation costs can unfortunately not be refunded. For more information, please contact Mr. Fruehauf, Tel.: +49 (0)89 7095 7800 (E-Mail: isd(a)med.uni-muenchen.de<mailto:isd@med.uni-muenchen.de>). HOW TO APPLY: Your application - preferably in electronic form - with the usual documents indicating the earliest possible starting date should be directed to: Klinikum der Universitaet Muenchen, Institute for Stroke and Dementia Research Markus A. Fruehauf, Managing Director ISD Heiglhofstr. 55 81377 Munich | Germany E-Mail: isd(a)med.uni-muenchen.de<mailto:isd@med.uni-muenchen.de>

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Questions about Qdec
by Paola Valsasina 06 Jun '11

06 Jun '11

Dear FS list, I have a couple of questions about QDEC toolbox. 1) If I perform a multiple regression model and I obtain a significant cluster of correlation, is it possible to extract the corresponding regression coefficient, in order to report the strength of this correlation at that point? 2) Is it possible to perform some kind of masking? (e.g., to quantify correlation with a metric only within cortical areas that are different between groups?) 3) Is it correct that it is not possible to overlay the results of different qdec models on the same brain within qdec toolbox, but that we have to use a different tool (e.g. freeview?) to overlay multiple sig.mgh images at the same time? Thank you for any help Kind regards, Paola ----------------------------------------------------------------- Dai il tuo 5XMILLE al San Raffaele. Basta una firma. Se firmi per la ricerca sanitaria del San Raffaele di Milano, firmi per tutti. C.F. 03 06 42 80 153. INFO: 5xmille(a)hsr.it - www.5xmille.org

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Commands missing in freesurfer directory
by ANN40＠pitt.edu 06 Jun '11

06 Jun '11

Hi all, I recently downloaded and installed freesurfer for a Mac PowerPC. I tried running recon-all on my data and an error message came up saying command not found for talairach_avi and many other commands. I looked in my /Applications/freesurfer/bin directory and that file wasn't there. All the commands that had worked such as mri_convert were. Does anyone know what could be causing this problem? Thanks, Ashley

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Wm segmentation problem
by Irene Altarelli 06 Jun '11

06 Jun '11

Dear Freesurfers, we are processing a dataset of children through recon-all, applying manual corrections when needed. For one subject, after manual correction and running autorecon2-cp, we observe errors in wm segmentation, bilaterally, with portions of gm included in wm - as can be seen in the attached picture. This concerns most of the coronal slices. We have been checking that control points were not misplaced and they look ok to us. What do you think is happening there and is there anything we can try before manually correcting these errors? Thanks very much in advance, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23

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freesurfer license
by carolina.mr 05 Jun '11

05 Jun '11

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How to refine the recon-all results from old version?
by Xinian Zuo 04 Jun '11

04 Jun '11

Hi, FSers We have lots of data run based on a previous version (see 5.0). Is there any way to refine them using the FS5.1 pipeline but not to re-run all steps of recon-all? Many thanks! -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)

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GUI analysis
by Carolina Valencia 03 Jun '11

03 Jun '11

Dear freesurfer users I want to know where I can find the GUI that assist in the management and analysis of groups of data not shown in the FreeSurfer Analysis Pipeline Overview Thanks, Carolina

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