Freesurfer July 2017

freesurfer@nmr.mgh.harvard.edu

118 participants
198 discussions

Using multimodal slab input for hippocampus subfield segmentation in FS6
by Frauke Beyer 05 Jul '17

05 Jul '17

Dear experts, I am trying to use T2-weighted images (0.5x0.5x1mm) as an additional scan to a T1-weighted image (0.7x0.7x0.7mm) for hippocampal subfield segmentation in Freesurfer 6. The T2-weighted data is a slab which includes the whole hippocampus and its y-axis is parallel to the hippocampal long axis (image dimensions [384,384,50]). When I try to use recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID>I always get a faulty alignment (through visual inspection by overlaying T2.FSspace.mgz on T1.mgz in freeview or by looking at the quality control image T1_to_T2.v10.QC.gif), even when I manually align the images beforehand. Do you have any idea or hint how to improve the registration and thus start the segmentation correctly? I also tried to find out which registration tool is used for this (mri_robust_register?) in order to play around with it and would also be thankful for any hint on this. Thank you for your advice and time, Best, Frauke

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Recon-all: too many ('s
by M del Mar Velasco 05 Jul '17

05 Jul '17

Dear all, I am running a recon-all with Freesurfer-Linux-centos6_x86_64-dev-20170330-de24995 and Ubuntu 16.04: recon-all -subjid subject_name -all I am using 0.65m3 images from RM. I get the message ' Too many ('s ' and the recon-all stops at Aparc-to-Aseg. The recon.all.log doesn't state anything about this message. The analysis just stops. I have attached the log file and the screenshot about the message. Any idea about the reason about this issue? And how can I solve it? Thanks you in advance M del Mar

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error message while using autorecon1
by Buckless, Colleen 05 Jul '17

05 Jul '17

Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks, Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 Buckless(a)kennedykrieger.org ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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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

1 1

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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Freesurfer July 2017