Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

Dilated ventricles
by Victor Kovac 01 Nov '13

01 Nov '13

Dear Freesurfer experts, I have run recon-all and included the -bigventrcles flag on a number of brains with ventriculomegaly. This fixed the segmentation errors in a few cases; however, there are still brains with dilated ventricles for which recon-all is not providing accurate segmentation (see attached image). Are there any other tricks I can attempt to solve this issue? I was considering doing manual pial and white matter edits in conjunction with filling the ventricles by using the Edit Voxels Tool. Would this be advisable? Thank you! Victor

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funcroi calculating percent signal change
by Alexandra Tanner 01 Nov '13

01 Nov '13

Hi Doug and Freesurfers, I would like to calculate percent signal change within an anatomical ROI for a group of subjects in Freesurfer 5.0. We are not functionally constraining our ROI, however, we do want to calculate the percent signal change across the entire region in each of our conditions (the contrasts we are using are condition-vs-fixation). Below are examples of the commands I've run for one of our conditions: funcroi-config -analysis SIRP_Stable5 -label lh.7Network_6.PFC.label -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg funcroi-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/18ActiveFolate_12Placebo_PreAndPost_7Tpost/lh_7Networks_6_PFC_1vFix -c Cond1vFix Is it necessary to now generate the mean functional baseline offset value within the ROI in order to calculate percent signal change if our contrast is comparing condition-vs-fixation? Any clarification on when the offset value is needed would be greatly appreciated! Thanks, Alex

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preferred method for generating appropriate bvecs for tracula
by Salil Soman 01 Nov '13

01 Nov '13

Hi, I have dicoms that I turn to nifti using dcm2nii (with the default settings plus anonymization option turned on [-a y]). The bvec files it generates by default are 3 rows by n columns (where n is b0 number + directions). I am under the impression tracula requires this to be converted to a n row by 3 column file. 1) is this correct, 2) is there a preferred way to perform this transformation on linux systems? Thanks you, -Sal

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How to generate histograms of intensities in one anatomical region?
by 赵越 01 Nov '13

01 Nov '13

Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate surfaces and labels in freesurfer. Then I would like to do statistical analysis in the regions I am interested in. For example, I would like to generate a histogram of intensities in frontal cortex or in occipital. I can display these regions in different color in freeview based on the look-up table but I don't know how to use them to generate histograms in freesurfer or create binary masks then I can do the analysis with these masks in matlab. I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create regional masks for a group study. I am new to freesurfer and I really appreciate if someone can point out a direction. Thanks! Best,Yue

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offset in QDEC
by Hamza Alshuft 01 Nov '13

01 Nov '13

Dear Freesurfers and experts Can any one please tell me what the offset box next to the max. box (under Threshold) in QDEC GUI is for? When I change from e.g 0 to 1 or higher I get larger significant clusters. How and when is this feature used? I also notice this very question is on the archive list but not answered. Here is the quote "Hi Bruce, I'm referring to "offset" in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is more larger. Stefano" Thanks Hamza 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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Re: [Freesurfer] R: Re: correction on question: offset in qdec GUI
by Hamza Alshuft 01 Nov '13

01 Nov '13

Hi Freesurfers! Has any one got an answer to this query asked sometime ago: > "Hi list, > I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And > what I can do using it? Hi Bruce, I'm referring to "offset" in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is more larger. Stefano" What the OFFSET next to the threshold max. is for? Kind regards Hamza 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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PhD position: Neuroimaging (MRI) in Epilepsy, University of Liverpool
by Keller, Simon 01 Nov '13

01 Nov '13

PhD Studentship in Specialised MRI in Medically Refractory Epilepsy £13,726 pa Stipend Department of Molecular & Clinical Pharmacology, Institute of Translational Medicine Location: University Campus Ref: PhD-MRI-refractory-epilepsy/WWW Closing date for receipt of applications: Thu, 07 Nov 2013 17:00:00 GMT A PhD Studentship is available in the Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine at the University of Liverpool, supervised jointly between Dr. Simon Keller and Professor Tony Marson. This is an exciting project that involves collaboration with the Walton Centre NHS Foundation Trust (WCFT), which is a specialist neurosciences NHS hospital providing a high quality, integrated, multidisciplinary neurosciences service to the northwest of England and North Wales. The multidisciplinary Epilepsy Research Group at the University of Liverpool and WCFT has a long-standing international reputation for assessing outcomes in people with epilepsy. People with medically refractory epilepsy who do not have a discernable brain abnormality on routine magnetic resonance imaging (MRI) pose a significant challenge in the clinical management of their disorder. Neurosurgeons are more hesitant to operate on people without an identifiable structural abnormality, and for people who do undergo surgery, postsurgical outcome is significantly poorer compared to people with a focal brain abnormality (e.g. hippocampal sclerosis). The focus of this project will be to use specialised MRI approaches with sophisticated image analysis techniques for people with refractory epilepsy who were found to be MRI-negative during routine clinical imaging in an attempt to identify brain alterations that may underlie the epilepsy disorder. You will perform manual and automated quantitative MRI (e.g. high resolution hippocampal measurements, analysis of cortical thickness), diffusion tensor imaging (DTI) and resting-state functional MRI analyses on data prospectively acquired for people with epilepsy and healthy controls. There is also the opportunity to analyse neuroimaging data that has been previously acquired. You will be expected to present your work at internal departmental meetings, national and international conferences, and as peer-reviewed manuscripts in internationally renowned journals. Applications are sought from graduates (First or Upper Second) in Neuroscience, Biomedical Science, Psychology, Medicine, or an equivalent discipline. Experience with MRI analysis techniques, particularly in context of a postgraduate qualification, is desirable. This studentship includes PhD tuition fees (UK/EU students only) and is available for three years. To apply please send a copy of your CV with covering letter to: Dr. Simon Keller (simon.keller(a)liv.ac.uk<mailto:simon.keller@liv.ac.uk>). -- Dr. Simon S. Keller Lecturer and Senior Scientist Neuroimaging The Department of Molecular and Clinical Pharmacology Institute of Translational Medicine University of Liverpool 2nd Floor, Neurological Science Clinical Sciences Centre Aintree University Hospitals and The Walton Centre NHS Foundation Trusts Lower Lane Liverpool L9 7LJ Tel: +44 (0)151 529 5943 Simon.Keller(a)liverpool.ac.uk<mailto:Simon.Keller@liverpool.ac.uk> www.liv.ac.uk/translational-medicine/staff/simon-keller/

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mri_glmfit-sim with conjunction maps but without pre-cached data
by Caspar M. Schwiedrzik 01 Nov '13

01 Nov '13

Hi, I have a question regarding cluster size thresholding using mri_glmfit-sim. Namely, I have a sig.nii conjunction map that I made with mri_concat. The analyses that serve as input to the conjunction map are done on a custom surface template. If I want to run mri_glmfit-sim, how would that work? I obviously do not have precached data. Thanks, Caspar

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Freesurfer November 2013