Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

Non-linear correlations
by mmoayedi 02 Aug '10

02 Aug '10

Hi Everyone, I was wondering if there's a method to examine non-linear correlations in FreeSurfer. Specifically, I'd like to use a behavioural correlate and see if there are any correlations in the cortex. The linear correlation wasn't as fruitful as I'd hoped, but there is evidence that a non-linear relationship may exist. Is there any way of testing this? Thanks. Regards, Massieh Moayedi PhD Candidate Dr. Karen Davis' Lab Institute of Medical Science University of Toronto MP14-303 Brain, Imaging and Behaviour Toronto Western Research Institute University Health Network 399 Bathurst St. Toronto, ON M5T 2S8 massih.moayedi(a)utoronto.ca mmoayedi(a)uhnres.utoronto.ca t: 416-603-5502 f: 416-603-5745

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Cerebellar hurdle
by Lena Palaniyappan 31 Jul '10

31 Jul '10

Is there any way I can recon-all for images that have cerebellum missing? These fail repeatedly at talairach, no-talcheck flag doesn¹t help Cheers thanks _______________________________________________________ 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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tkmedit scripting question
by Sebastian Moeller 30 Jul '10

30 Jul '10

Aloha fellow surfers, I am trying to script a few steps of my freesurfer pipeline. At the moment I am facing the problem that all my brainmasks need some manual intervention. Following advice from the wiki I try to set up tkmedit to clone from the aux to the main volume on the pressing button 3. Now my question how do I configure Button 3 from a tcl script so that my users do not have to do this manually every time? I would expect something like SetBrushInfo that takes more arguments than just brush, low, high, new, but my tcl-foo is very weak. If someone has a pointer how to set Button 3 to clone from aux vol I would be happy to hear it. Thanks in advance. Best Sebastian -- Sebastian Moeller telephone: 626-395-6713 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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spmregister error
by swoodman＠nmr.mgh.harvard.edu 30 Jul '10

30 Jul '10

Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed __________________________________________________________ Our information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons PWD: /cluster/ablood/1/DMRF_ASL ssh purkinje setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd /cluster/ablood/1/DMRF_ASL __________________________________________________________________ We appreciate any help you can give us!! Thanks, Sandra Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital 120 6th St. Charlestown, MA 02129 Tel: 617-643-6245 Fax: 617-726-1351 Email: swoodman1(a)partners.org

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more thinner parcelation borders
by Gonzalo Rojas Costa 30 Jul '10

30 Jul '10

Hi: I change the color palette of the parcelation borders to white... But, I need thinner parcelation borders... can I change that parameter ?... Or could I specify a transparency factor for the borders ?... Sincerely, Gonzalo Rojas Costa

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[fsfast]: temporal overlap of stimuli and concurrent presentation
by Sebastian Moeller 30 Jul '10

30 Jul '10

Dear fellow Surfers, is it possible to model several independent event streams for fs-fast? That is, using the 5 column paradigm file, is it okay to have different condition ID codes that have identical stimulus onset time (well only some of the time)? Or would I have to model that by specifying a TER and have both staggered around the real onset time? I would be happy to receive any pointer. Thanks in advance & best regards Sebastian -- Sebastian Moeller telephone: 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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Methods for white matter hypointensities measure
by Laluz, Victor 30 Jul '10

30 Jul '10

Hello guys, I am curious as to how white matter hypointensities (on T1 mprage) are measured automatically for the aseg.stats file in FS? A group at UCSF is interested in using this measure for a study and would like to have a nice explanation or citation to describe how it is generated. I have looked through what I think the likely citations would be on the Freesurfer techniques article listing and came up empty. Thanks! Victor Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center

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Motor areas from Talairach
by Ben Hamida Cammoun Leila Faiza 30 Jul '10

30 Jul '10

Hi I am trying to find different Talairach areas in the motor cortex. I used the mris_convert -t function on the inflated brain (.asc). I selected coordinates using ranges from a paper (for example range x -70 to 4; range y -43 to 7 and range z 19 to 76 for M1). But when I want to see if they are in the wright area with tksurf on the same surface (inflated), the coordinates change. Do you know how to find the wright coordinates? Thanks Leila

2 1

monkey brain recon outputs
by Arslan, Ali 29 Jul '10

29 Jul '10

Hi, I finished reconstructing a monkey's surface following the scripts on the wiki. The output surfaces seems to be a bit distorted and rough around the edges. This reconstruction is done with a volume normalized by using ~400 white matter control points. The resolution of the scan is 1x1x1 mm. Here are some pictures to look at: http://www.flickr.com/photos/52445793@N05/sets/72157624471174691/ Interestingly, white matter and gray matter boundaries seem to be intermingled for some reason. I was hoping control points would take care of that problem but they didn't. This can be observed by the 2 vol_surf images in the set. The most obvious defects can be seen on the white matter. There are small protrusions over the gyri, and the surfaces are generally very rough, unlike a successful human reconstruction. I was wondering if you have any ideas as to the source of the problem. Skull stripping was done with FSL's bet, and it looks successful. Can it be a problem with intensity normalization? Regards, Ali Arslan

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Overlay Thickness Files in tkmedit
by Michael Scheel 29 Jul '10

29 Jul '10

Hi, is there a way to visualize the lh.thickness or rh.thickness files as an overlay in tkmedit. Thanks, Michael

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Freesurfer July 2010