Freesurfer January 2011

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School
by sheraz＠nmr.mgh.harvard.edu 03 Jan '11

03 Jan '11

Postdoctoral Fellowship: Multimodal Neuroimaging Description: A postdoctoral position pursuing multimodal imaging is available with the TRANSCEND Research Program (www.transcendresearch.org) at the Martinos Center for Biomedical Imaging in Charlestown, MA (www.martinos.org) which is affiliated with the Massachusetts General Hospital, Harvard and MIT. There is a second location at a clinical site, the MGH-affiliated Lurie Family Center for Autism, where we have a 128 lead EGI EEG in a shielded room as well as a photogrammetry machine and autonomic monitoring equipment, and will shortly have a near-infrared tissue spectrometer (NIRS) machine. The programs emphasis is on pathophysiologically oriented brain research and application of advanced imaging acquisition and analysis techniques to neurological and sensory aspects of autism spectrum disorders. Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL), on co-registering EEG and MEG with MRI, and on studying neurovascular coupling with EEG and NIRS. This position will involve analysis of existing multimodal imaging data and collection of new data. It will involve working closely with a multidisciplinary team and with children, and will also involve some research oriented analysis of data collected for clinical purposes. The age range of our subjects is primarily from early infancy to mid-adolescence, with some additional studies including young adults. An ample opportunity will also be provided to the candidate to self-explore and lead research. Requirements: Candidates must have PhD in neuroscience, physics, biomedical engineering, electrical engineering, computer science or other related fields. Candidates without this training and experience need not apply. Prior experience in MRI analysis and EEG signal processing is required. Salary will be consistent with Massachusetts General Hospital, Harvard Medical School policies for Postdoctoral trainees and will range between $45,000 to $55,000 depending upon qualifications and experience. Compensation also includes full staff benefits, including health insurance, and vacation time. Contact: Interested applicants may send a CV and statement of interest addressing background and specific pertinence of the candidates interest to Dr. Martha R. Herbert at mherbert1(a)partners.org and cc transcend(a)partners.org. Applications will be considered until the position is filled.

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(no subject)
by FIDEL ALFARO ALMAGRO 02 Jan '11

02 Jan '11

Happy holidays for those who celebrate it today, Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any. Thanks in advance.

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cortical thickness of a ROI
by angela.favaro＠unipd.it 02 Jan '11

02 Jan '11

Dear all, I have not received any advice about this point. Can somebody help me? thank you! I followed the instructions found in Freesurfer tutorials ('cortical thickness of a volume-defined ROI'). However, in the point 4 of the procedure I am not able to change the --reshape default. My run is: mri_surf2surf --s subj001 --trgsubject fsaverage --hemi rh --sval rh.thickness --tval rh.thickness.fsaverage.mgh --reshape-factor 7 but it continues to create (like default) a reshape with 6. For this reason, I think, the following command: mri_segstats --seg $SUBJECTS_DIR/rh.fsaverage.mask21.mgh --in rh.thickness.fsaverage.mgh --sum segstats-mask21.txt give: ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 What can I do to solve this problem? Thank you for your help! Angela Angela Favaro, MD, PhD, MSc Psychiatric Clinic Department of Neurosciences via Giustiniani 3 35128 Padova Italy

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Interpreting results from Qdec
by Gallen, Courtney (NIH/NIDA) [F] 02 Jan '11

02 Jan '11

Hi, I'm currently running analyses in Qdec and have identified areas that show significant effects in my contrasts. I have two questions related to interpreting these results. 1. How can you interpret the effect in each "blob?" (i.e., which group has a greater cortical surface area, etc.). Right now, all I know is that there is an effect in certain areas. Can you export this data to get means and standard errors? 2. Is there a way to localize where these effects are? E.g., a tool that tells you this effect is located in __ area of the brain? Thanks in advance Courtney Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631

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Smoothing fwhm.dat
by Joana Braga Pereira 02 Jan '11

02 Jan '11

Dear all, I have a question regarding smoothing in qdec. >From what i've understood from previous emails, for monte carlo simulations qdec calculates the best smoothing for your data set, saving it in the file fwhm.dat. How does it calculate this smoothing? Many thanks, Joana

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Getmatlab
by Lena Palaniyappan 02 Jan '11

02 Jan '11

I have MATLABR2010b, on a Mac 10.6.4, using freesurfer 5.0 I am not able to getmatlab when I invoke freesurfer Can someone help? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. 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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merging average cortical thickness data
by tina roostaei 02 Jan '11

02 Jan '11

Dear all, I have access to a dataset of freesurfer segmentation products (i.e. cortical volume, surface area, cortical thickness average and standard deviation) for a number of patients. I wanted to merge the data of some segmented parts (e.g. to compute a general cortical thickness average for the inferior frontal gyrus using the pars orbitalis, pars opercularis and pars triangularis data). I wanted to know if it is right to compute the average cortical thickness using the following formula: Average cortical thickness= [(part 1 cortical thickness*part 1 surface area) + (part 2 cortical thickness*part 2 surface area) + …]/ (part 1 surface area + part 2 surface area + …) BTW, I also checked whether the cortical volume equals ‘surface area*average cortical thickness’, to see if I could use the following formula instead: Average cortical thickness= (part 1 cortical volume + part 2 cortical volume + …)/ (part 1 surface area + part 2 surface area + …) But it simply proved wrong. Any suggestion is greatly appreciated. Thanks in advance. Tina

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QA on wmparc.mgz
by Jeff Sadino 02 Jan '11

02 Jan '11

Hello, I am trying to verify the wmparc.mgz segmentations. I have identified outlier regions statistically, but then when I load up the wmparc.mgz file to QA visually, I find it is very difficult to QA the white matter regions. The problem is that because there is no contrast in the white matter, it is difficult to decide where one region ends and another one begins. I would like to ask if anybody has any suggestions as to a better way to visually verify the wmparc.mgz file. Thank you, Jeff

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Subtracting thickness maps
by Lena Palaniyappan 02 Jan '11

02 Jan '11

I have two groups - in each of the groups I have studied the relationship between a variable of interest and thickness. I want to show a subtraction between the two thickness correlation maps to highlight the regions with differing relationships with the variable in the two groups. In other words, I want to generate a single image on an average surface, that shows the regional differences between the correlated thickness maps. Is this feasible? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. 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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Alignment of non whole-brain functional slabs
by Joakim Vinberg 02 Jan '11

02 Jan '11

Hi everybody, I am working towards multi-modal integration of BOLD data. For some of my data, the entire brain was not recorded (in this case, I have 12 slices covering the superior half of the brain). I have been working to align this data using bbregister and have had very inconsistent results: in 1 subject it worked great; in another 6, the alignment failed (resulting in an alignment that is sometimes close, and sometimes way off). I am creating a .nii using MRICRON/dcm2niiGUI, and using bbregister. I have used this method successfully with a number of other sessions so far (with functional slabs that do cover the entire brain) with outstanding results. Is this troublesome for bbregister, or is there potentially something I'm doing incorrectly? Thanks in advance! If I'm repeating well-worn topics, I apologize, I couldn't find anything following a search through the archives. Joakim

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Freesurfer January 2011