Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

multiple comparison correction using monte carlo
by Casper van Oers 05 Feb '10

05 Feb '10

Hi, I have performed a linear mixed model analysis on surface data in AFNI using SUMA, resulting in each vertex having a p value. I would like to perform a multiple comparison correction using freesurfer, as an FDR approach in AFNI is to stringent (individual vertex statistical thresholds are low). I would like to run a monte carlo simulation using mri_glmfit on a similar surface with similar parameters to extract a cluster threshold. I am not used to using freesurfer, so bear with me, please. 1) I have created a fsgd file defining the structure of the analysis used. This seems to be the tricky part, as I don't know how to exactly specify the model used. Maybe it suffices to define the data structure. There is two groups (patients, controls) and three timepoints. I want to correct for the group between group difference (contrast 1 -1), but don't know how to specify multiple timepoints per subject. 2) I have smoothed the data with fwhm 3mm in afni. How can I perform the simulation using mri_glmfit-sim and how can I do this without doing the analysis itself in freesurfer? I would appreciate your advice! Casper -- Casper A.M.M. van Oers, MD Department of Neurology, C03.236 University Medical Centre PO Box 85500 3508 GA Utrecht the Netherlands T: +31 30 2503184 F: +31 30 2542100 (Dept. of neurology)

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mri_diff geometry differences
by Michael Harms 04 Feb '10

04 Feb '10

Hello, What do "geometry differences" represent in the output of mri_diff? i.e., What do the numbers in the following output from mri_diff represent? Volumes differ in geometry 1 4 0.000015 Volumes differ in geometry 2 1 0.000000 thanks, -Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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RES: Re: how to QC hippocampal measurement
by "Pedro Paulo de Magalhães Oliveira Junior" 04 Feb '10

04 Feb '10

In our AD paper (Journal of Alzheimer's disease) has some standard values for AD and non-demented -- @mobile -----Msg original----- De: Nick Schmansky Enviado: 04/02/2010 17:07:02 Para: Guang Zeng Cc: freesurfer(a)nmr.mgh.harvard.edu Assunto: Re: [Freesurfer] how to QC hippocampal measurement a simple way is to just plot the values. if a segmentation is horribly wrong, then its value will be way out of bounds compared to the others. note that there will be quite a bit of variation in size because of the AD subjects, so this method is just a simple QC. n. On Thu, 2010-02-04 at 12:58 -0600, Guang Zeng wrote: > Hi, there, > > I have used FreeSurfer to measure the hippocampal size of 200 ADNI > subjects, and now I'd like to QC the hippocampal measurement. > Anyone can give me some suggestion to do this, instead of loading they > one-by-one ? > > Thanks! > Guang > > > ______________________________________________________________________ > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up > now. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Research Assistant Position
by Victoria Williams 04 Feb '10

04 Feb '10

Two Research Assistant Positions in Neuroimaging of Traumatic Brain Injury and Post Traumatic Stress Disorder: Boston, MA, 02130, USA Employer: VA Boston Healthcare System Tags: Neuroimaging Neuropsychology/neuropsychological assessment/cognitive neuroscience Traumatic Brain Injury Post Traumatic Stress Disorder MRI, DTI, FMRI, ASL Programming Research assistant/RA PLEASE REPOST FOR INTERESTED PARTIES Job Description: The VA Boston Healthcare System and the VA Boston Neuroimaging Center invite applications for a research assistant position in neuroimaging of Traumatic Brain Injury (TBI) and Post Traumatic Stress Disorder (PTSD). This is a position within the newly funded VA Rehabilitation Research and Development Service TBI Center of Excellence Entitled "Translational Research Center for TBI and Stress Disorders (TRACTS)". Responsibilities will include acquisition and analysis of a range of magnetic resonance imaging (MRI) data collected for the TRACTS research program (including structural MRI, DTI, fMRI, and ASL). A second position will be focused more on technical infrastructural support for investigators involved with this project. TRACTS is a unique longitudinal study of over 300 Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF) returning service members focused on understanding the neurological and cognitive consequences of blast exposure and differentiating the effects of blast from those of post traumatic stress. Experience in computer programming (Linux/Unix shell scripting and MATLAB), neuroimaging analysis methods (FSL, Freesurfer), and some statistical experience would be a plus. This position requires a minimum of a two year commitment (with opportunity for a longer position), and is available beginning immediately. Salary will be consistent with levels in accordance with the Boston VA Medical Center policies for research assistants. This is an optimal position for an individual who would like to obtain research experience before applying to graduate programs, or individuals that are looking for a more long-term position. Compensation includes full staff benefits, including health insurance, and vacation time. To apply or request more information, please send a CV and other relevant information to Dr. David Salat salat*at*nmr*dot*mgh*dot*harvard*dot*edu with the subject line "TRACTS RA position".

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Postdoctoral Position
by Victoria Williams 04 Feb '10

04 Feb '10

Postdoctoral Position in Neuroimaging of Traumatic Brain Injury and Post Traumatic Stress Disorder: Boston, MA, 02130, USA Employer: VA Boston Healthcare System Tags: Neuroimaging Neuropsychology/neuropsychological assessment/cognitive neuroscience Traumatic Brain Injury Post Traumatic Stress Disorder MRI, DTI, FMRI, ASL Programming Postdoctoral/postdoc PLEASE REPOST FOR INTERESTED PARTIES Job Description: The VA Boston Healthcare System and the VA Boston Neuroimaging Center invite applications for a postdoctoral research scholar position in neuroimaging of Traumatic Brain Injury (TBI) and Post Traumatic Stress Disorder (PTSD). This is a position within the newly funded VA Rehabilitation Research and Development Service TBI Center of Excellence Entitled "Translational Research Center for TBI and Stress Disorders (TRACTS)". Responsibilities will include analysis of a range of magnetic resonance imaging (MRI) data collected for the TRACTS research program (including structural MRI, DTI, fMRI, and ASL), as well as independent research that fits within the TRACTS framework. TRACTS is a unique longitudinal study of over 300 Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF) returning service members focused on understanding the neurological and cognitive consequences of blast exposure and differentiating the effects of blast from those of post traumatic stress. A variety of additional information will also be collected, including neuropsychological and psychiatric scales, medical history interviews, and a range of physiological information. Imaging sessions will take place on the Neuroimaging Center's 3T Siemens TIM-Trio scanner and data collected includes high-quality structural, diffusion, and functional MRI data. The successful applicant will join a multidisciplinary team of researchers examining a range of sequelae affecting returning service members. Experience in computer programming (Linux/Unix shell scripting and MATLAB), neuroimaging analysis methods (FSL, Freesurfer), and advanced statistical analyses would be a plus. This position requires a minimum of a two year commitment (with opportunity for a longer position), and is available beginning immediately. Salary will be consistent with levels in accordance with the Boston VA Medical Center policies for Postdoctoral trainees. Compensation includes full staff benefits, including health insurance, and vacation time. To apply or request more information, please send a CV and other relevant information to Dr. David Salat salat*at*nmr*dot*mgh*dot*harvard*dot*edu with the subject line "TRACTS Postdoctoral position".

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a question about mris_ca_train
by Guang Zeng 03 Feb '10

03 Feb '10

Hi, there, Recently, I sent sseveral emails to you to ask same kind of question about building our own template and atlas. Thanks a lot for your quick reply, they helps me a lot. Currently, I still have a question about building our own atlas using mris_ca_train, sorry to bother you again. We have a surface labeling atlas in our lab, we'd like to use this atlas instead of using FS's desikan_killiany.2007-06-20gcs. It is kind of difficult for us to load every subject in our training set to tksurfer, and manually label each ROI based on our ATLAS. What we try to do is: 1. Send each subject in the training set to our toolbox which will use our atlas to do surface labeling. For each subject it will output a file just like wmparc.mgz in FS, but it is NIfTI file. 2. Send each subject to FS pipeline to get the ?h.sphere.reg, ?h.sulc files. 3. Find a method to get my ?h. mylabels. annot files, and use mris_ca_train to build a new atlas. First of all, do you think what I try to do is reasonable? If yes, I know I need to get the FS .label files for each ROI, then I can call mris_label2annot to get ?h. mylabels. annot files. But how can I get the FS .label files for each ROI from our toolbox output ROI labeled NIfTI file? These qurstions trouble me for a long time, your help are really appreciate. Thanks a lot! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/

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where can I find write_annotation.m
by Guang Zeng 03 Feb '10

03 Feb '10

Hello, there, Where can I download write_annotation.m, I can not find it in my /matlab folder. Thanks! Guang _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/

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Re: [Freesurfer] recon-all -mprage flag
by Judith Segall 03 Feb '10

03 Feb '10

Hi Freesurfer users. I recently noticed the "-mprage" option when running recon-all. Is this the same multi-echo mprage developed by Andre van der Kouwe? Also, what are the advantages for using the -mprage option if you are using the mgh developed mprage? Thanks, Judith S Mind Research Network

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FreeSurferColorLUT label Unkown in annotation file
by Guang Zeng 03 Feb '10

03 Feb '10

Hi, there, I have question about FreeSurferColorLUT label Unkown in annotation file. In FreeSurferColorLUT, I read that #No. Label Name: R G B A 0 Unknown 0 0 0 0 I load the inflated surface of a subject, import lh.aparc.annot file. All the subcortical region are labelled as "Unknown" Then I load the lh.aparc.annot file using read_annotation.m to MATLAB as [vertices, label_val, colortable] = read_annotation(annotation_filename); Since the RGB of label Unknown is zero, then its label value in read_annotation.m should also be zero, since annotation value = (R) + (G * 256) + (B * 256^2) However, there are no vertices with label_val = 0 when I use unknown = find(label_val == 0). I also check the label_val of several randomly picked verteices in unkown (subcortical) region, they gave me different values. I thought I should find the same values, although they may not equal to zero. So, my question is how to find the vertices which are labelled as unknown in annotation file? Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/201469226/direct/01/

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scrambled boundaries
by Brendan Robert Ansell 02 Feb '10

02 Feb '10

Hi, I have a set of fairly old MRIs which have been run on freesurfer. Occasionally scans have scrambled pial or white matter boundaries - a knot-like appearance especially in sulci. I am wondering how freesurfer estimates cortical thickness in these regions. For example, does it take the pial boundary closest to the white boundary i.e. the outer surface of the 'pial knot'? Are the encapsulated GM voxels included in the overall cortical thickness measurement? Thanks- Brendan Ansell MNC

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