Freesurfer

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30090 discussions

Additional surface area
by Michael Davies 05 Jul '17

05 Jul '17

Hello, when inspecting a subject i discovered an anomaly on top of the 3D surface i have not previously encountered on other subjects i have inspected. Could you please let me know if this would be problematic when at the analysing group data please? Kind regards, Michael

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Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0 - with links to files
by Torben Lund 05 Jul '17

05 Jul '17

Hello FreeSurfer Developers I'm attempting to evaluate a segmentation result from CAT12, (sorry) with the Freeview program. For version 1.0 superimposing a gifti surface on top of a nifti volume works beautifully (see results here: https://www.dropbox.com/s/lwhonnzy7n2t87x/Freeview1.0.pdf?dl=0 <https://www.dropbox.com/s/lwhonnzy7n2t87x/Freeview1.0.pdf?dl=0> ), but with the new version 2.0 the orientation is messed up (see result here: https://www.dropbox.com/s/ma6p4batv2cc6w4/Freeview2.0.pdf?dl=0 <https://www.dropbox.com/s/ma6p4batv2cc6w4/Freeview2.0.pdf?dl=0> ), for the exact same files. Has anybody else experienced this problem, and could it potentially be caused by recent changes in the minc tools which nifti converter I know have been changed between the two Freeview versions. The issue seems to be platform independent and exist for both MacOS 10.12.15 and linux (Ubuntu 16.04.1 LTS) Best Torben Torben Ellegaard Lund Associate Professor, PhD Center of Functionally Integrative Neuroscience (CFIN) Aarhus University Aarhus University Hospital Building 10G, 5th floor, room 31 Noerrebrogade 44 8000 Aarhus C Denmark Phone: +45 7846 4380 Fax: +45 7846 4400 http://www.cfin.au.dk <http://www.cfin.au.dk/> torbenelund(a)cfin.au.dk <mailto:torbenelund@cfin.au.dk> (for official stuff) torbenelund(a)me.com <mailto:torbenelund@me.com> (for faster response)

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Speeding up mri_robust_register with --cost ROBENT
by Michael Waskom 05 Jul '17

05 Jul '17

Hi Freesurfers, I'm using mri_robust_register to obtain a registration between high resolution (.7mm isotropic) whole-head T1w and T2w images from the same subject. An example command line is: mri_robust_register --mov T2w.nii.gz --dst T1w.nii.gz --lta T2w_to_T1w.lta --warp T2w_reg.nii.gz --cost ROBENT --entradius 2 --entcorrection --satit --iscale This works extremely well -- much better than FLIRT. (I'm using this registration to do some preprocessing before running recon-all, so unfortunately bbregister is not an option). But, it takes *forever*. (My runtimes are about 90 minutes using OMP parallelization with 24 cores, or about 16 hours running in serial). I'm interested in playing with the various options to see if I can get a suitable registration with a faster runtime. But it's not obvious to me how I should fiddle with the knobs to get started. For example, would increasing or decreasing `entradius` be expected to make things go faster? Also, I am acquiring the images in the same session, back to back, so I can assume that the images start off with a pretty good (but not exact) registration. Is there a way to use that assumption to speed things up? Thanks, Michael

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Convert mgz figure
by shi yao wang 05 Jul '17

05 Jul '17

Dear FS expert, Is that possible to extract .jpg or .tiff files by using command line? Or convert .mgz file to other format file? If ok , then I can write a program to do this action automatically. Thanks Lawrence

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To get postings
by vittal korann 05 Jul '17

05 Jul '17

vittalkorann(a)gmail.com *Best* *Vittal*

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Effect of continuous time-varying covariate across time in LME models
by Matthieu Vanhoutte 05 Jul '17

05 Jul '17

Dear Freesurfer’s experts, I would like to test if neuropsychological score across time (continuous time-varying covariate) has an effect on metabolism maps. However, I don’t manage to understand how to define design matrix and contrast associated to assess it with LME models. I picked up from one former mailing list discussion including Jorge: we recommended to order the columns of the design matrix in the following way: Column 1: the intercept term (which is a column of ones) Colum 2: the time covariate if it varies across subjects (eg. time from baseline) Column 3-q: any time-varying covariates (eg. training: 0 before training, 1 after training) Column q+1-r: the group covariates of interest (eg. a binary variable indicating whether or not the subject is a patient), for n groups you will have n-1 binary covariates Column r+1-s: interactions between group covariates with the time-varying covariates (only the interesting interactions) Column s+1-p: any other nuisance time-invariant covariates (eg. age-at-baseline, gender, etc...) 1) If I apply these advices, I would define in Column 3 my neuropsychological scores as my time-varying covariate but should I have to normalize these scores ? 2) If I want to correlate my metabolic maps (inputs) with my neuropsychological time-varying covariate should I have to define a column of interaction between neuropsychological time-varying covariate and (group or time) ? 3) How should I define contrast matrix to assess this effect ? Thank you for your advices !! Best regards, Matthieu

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sulcus in the orbitofrontal wm
by Manuel Delgado 05 Jul '17

05 Jul '17

Dear list: We are editing wm and facing a problem we do not know how to solve. In the orbitofrontal wm there is a sulcus that has been fully included into the wm boundary. However there is not wm mask to be erased. I have uploaded the file 40_001 and I would be grateful if could take a look. This problem is located on coordinates Talairach (wm) 110.66, 158.70, 165.37 In addition, there is an hyperintensity in the extreme of the orbitofrontal wm we would like you to take a look and work out the best solution (I gess control points would fix it?) This is on coordinates 111.29, 161.59, 178.55. Thanks in advance -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n* *39011 Santander, Spain*

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lopsided hemisphere
by Michael Davies 04 Jul '17

04 Jul '17

Hello, I have encountered a lopsided hemisphere when analysing the data. What procedure do i need to employ to fix the problem? Any advice would be greatly appreciated! Kind regards, Michael

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Anterior and posterior insula in fsaverage space
by Juergen Haenggi 04 Jul '17

04 Jul '17

Dear FS experts I am wondering whether there exist labels of the insula other than that provided by aparac and aparc.a2009s. I am searching for labels of the anterior and posterior insula in the fsaverage space. I have drawn such regions (see attachment), but these are rather subjective. Any suggestions are welcome. Thanks in advance Regards Jürgen Hänggi ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. -----------------------------------------------------------------------------------------------------

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Re: [Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter
by Vincent Koppelmans 03 Jul '17

03 Jul '17

Hi Bruce, Thank you for your reply. The aseg seems to be okay: https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0 <https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0> Do you have any other suggestions? Here is an extra image of the cortical ribbon. Maybe this helps: https://www.dropbox.com/s/ycav96v91e4ncbg/Cortex.png?dl=0 <https://www.dropbox.com/s/ycav96v91e4ncbg/Cortex.png?dl=0> Thanks! - Vincent On Mon, 03 Jul 2017, Bruce Fischl wrote: Hi Vincent the putamen error probably means that the aseg is wrong, and if so, you can correct the aseg and rerun autorecon2-wm and autorecon3 I believe. For the medial ttemporal lobe issue is that really cortex? I can't really tell from the single coronal slice. I'll cc Jean Augustinack to see if she has an opinion. cheers Bruce On Fri, 30 Jun 2017, Vincent Koppelmans wrote: Hi all, I was wondering how to fix the following issues: 1) The cortical ribbon extends into the gray matter of the putamen (see the top row of the attached image). 2) Cortical gray matter is missing in the medial temporal lobes (see the bottom row of the attached image). I can’t find solutions for these particular issues under https://surfer.nmr.mgh.harvard.edu/fswiki/Edits <https://surfer.nmr.mgh.harvard.edu/fswiki/Edits> <https://surfer.nmr.mgh.harvard.edu/fswiki/Edits <https://surfer.nmr.mgh.harvard.edu/fswiki/Edits>> How should I approach this? Suggestions are very much welcome. Thank you! - Vincent

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