Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

Looking for advices on the best parameters to use with a Montecarlo cluster-wise correction
by Damien MARIE 03 May '17

03 May '17

Hi, I would like to get your opinion about Montecarlo statistics. I know that there is maybe not a simple answer and that it depends probably on the research question but anyway, is there some kind of gold standard about the number of montecarlo simulations / p values ? Speaking about that with colleagues, I had plenty of divergent opinions for both variables depending on their neuroimaging field i.e minimum 10,000 / 3,000 / 1,000 simulations - minimum p < 0.05 / 0.001 (the latest threshold being advised on the basis on the recent papers on false positives) . I am also wondering if it makes sense to use this correction as a "SPM-like small volume correction". What I mean by SPM-like small volume correction, is when you got clusters in a region for which you have an apriori hypothesis, that they do not survive to multiple comparisons, and you restrain your analysis to the region of interest. In my study, it would be 1 or 2 merged labels from the auditory cortex. Thank you for your input, Best, Damien

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Consistent volume increases for some regions when using longitudinal stream
by Melanie Ganz 03 May '17

03 May '17

Dear list and especially Martin, we have used Freesurfers crosssectional as well as the longitudinal stream and are inspecting the outcomes at the moment. We have as quality assurance been inspecting regions where the difference between initial CROSS results and the corresponding LONG results exceeds 10 %. In this process we found that for certain regions it seems that the volume increases in almost every case. Below is an overview of differences between cross and long with mean, sd, max and min values in percent for different regions. We also manually checked an example of the Caudate where there was an increase of 14 % from CROSS to LONG. This difference can be seen between CROSS to LONG for time point 2. It seems like the longitudinal is correct when it covers more of the Caudate. The other time point for that subject and their base seems to provide extra information which is a good thing. However our question is why this seems to be a systematic thing that all scans for the caudate region increases in volume when doing the longitudinal processing? This is also the case for some other regions as seen below. Kind regards/ Melanie and Mark ---------------------------------------------------------------------------------- Percent volume changes between CROSS and LONG over 110 subjects: Region Mean Sd Max Min Estimated brain Volume 1 4 32 -18 Total Gray Matter Volume 1 1 5 -2 White Matter Volume -1 1 2 -5 Caudate 5 2 14 0 Putamen 8 3 22 1 Thalamus 2 3 13 -10 Amygdala -1 4 33 -8 Hippocampus 1 4 33 -5 Ventricles 0 2 5 -5 Frontal 0 2 6 -7 Parietal 2 2 8 -6 Temporal 1 2 5 -5 Occipital 1 2 9 -5

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Long-stream comparing differing resolutions
by Adam Martersteck 03 May '17

03 May '17

Dear FS Experts, I’m trying to compare multiple T1-weighted sequences taken across multiple scanners in the same day in 15 individuals using the longitudinal stream. One question we had was how different cortical thickness estimates would be using a 0.8mm^3 resolution vs. our standard 1mm^3 MPRAGE. Unfortunately, during the initial long-stream norm fusion, the –hires enabled 0.8mm data has a mismatch in dimensions compared to the standard 1mm data. Given this limitation -- what would be the best way to compare these two sequences? Thanks, Adam

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Converting tkr CRS to native CRS
by Burke Rosen 02 May '17

02 May '17

How can I get the the position of a tkr voxel in terms of the native voxel space? My guess was: pos = Torig*[C R S ones(size(S))]';% orig CRS to tkrRAS pos = P*pos;% tkrRAS to native RAS pos = W*bmsk;% native RAS to native CRS Where, Torig is given by mri_info --vox2ras-tkr orig.mgz P is qiven by mri_info --tkr2scanner orig.mgz W is given by mri_info --ras2vox orig/001.mgz But that is not returning expected values. Thank you, -Burke Rosen

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Setting -openmp flag to more than 8
by Chris Gorgolewski 02 May '17

02 May '17

Hi, We are running freesurfer as part of a bigger pipelines with other steps that can be performed in parallel to freesurfer reconstruction. So far we have set the openmp flag to the number of all available cores. However, our experience with ANTs and AFNI which also capitalize on the OpenMP parallelization is that there is little benefit of using more than 8-10 cores (even if more are available). Does this also apply to FreeSurfer? Does anyone have done some benchmarking of this? Thanks in advance for your help. Best, Chris

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Post-doctoral Position in Multimodal Brain Image Analysis of Age-Associated Disease in Boston, MA
by Leritz, Elizabeth C. 02 May '17

02 May '17

The Vascular Risk and Cognition laboratory in the Neuroimaging Research Center at VA Boston and Harvard Medical School is recruiting a full-time postdoctoral fellow with expertise in magnetic resonance imaging (MRI) and strong data processing skills. The postdoctoral position will focus on the application of structural and functional MRI to examine biomarkers of cerebrovascular disease in middle and older-aged adults. Duties will include MRI scanning, data processing and analysis, statistical analyses (general linear models, regression, and multivariate statistics), scripting (C, MATLAB and unix) as well as database creation and management. The position will also involve some administrative duties. The successful candidate will have a doctoral degree in cognitive neuroscience, neuropsychology, biomedical engineering or a closely related field, and substantial experience in MRI data acquisition (structural and functional MRI) and data processing. Experience in processing data from breath-hold paradigms a definite plus. Candidate should have expertise working with MRI analysis software such as Free Surfer and FSL as well as familiarity with unix/linux, MATLAB, and scripting. Candidate should also have good writing skills as manuscript preparation and publishing is expected. Experience with neuropsychological research, including interpreting cognitive data, is a plus. Dr. Betsy Leritz will be the primary mentor and the fellow will also collaborate with Drs. David Salat, William Milberg, and Regina McGlinchey. The postdoctoral fellow will interact with several research groups within the Neuroimaging Center who are examining age-related brain and cognitive changes, and will also have intellectual opportunities at Harvard Medical School and VA Boston Healthcare System. The start date is September 1, 2017. A minimum two-year commitment is required. Salary is consistent with NIH and Harvard Medical School guidelines for postdoctoral fellows. Interested candidates should email a single PDF containing a letter of interest as well as a CV. All materials should be sent to Dr. Betsy Leritz at elizabeth_leritz(a)hms.harvard.edu<mailto:elizabeth_leritz@hms.harvard.edu>.

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Freeview GUI Display Issues
by Kevin Japardi 02 May '17

02 May '17

Hello Freesurfer! I'm working with someone in our group on some Freesurfer QA, and she's having some issues with using the freeview gui. She's using a Mac with OS Sierra, with X11 2.7.8. Some of the issues she's having are: 1) The Mac red-yellow-green 'exit/hide/extend' buttons are blackened out in a black rectangle at the top of the window. 2) When switching axis views, the 3D view box remains stuck on the window, obscuring a good portion of the viewer screen. Also to note: files loaded (e.g. volumes and surfaces) load and view correctly. From her computer, I logged onto our server, and the viewing bugs still resided. Using my own computer, everything works fine. I'm running X11 2.7.8, but with OS Yosemite. Both of us are using Freesurfer v5.3.0. Apologies if this question is redundant, and I don't know if other's have had this issue. Please let me know if there are any thoughts on this. Thank you, Kevin Japardi

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Volume vs cortical thickness
by John Anderson 02 May '17

02 May '17

Dear Freesurfer experts, I highly appreciate if anybody clarify how Freesurfer calculate cortical thickness and gray matter volume. If the cortical thickness of e.g. precentral gurus is measured as the closest distance from the gray-white boundary to the gray-CSF boundray at each vertex on the tessellated surface (Fischl and Dale. 2000). How the gray matter volume for the precentral gyrus was measured? Thank you for any clarification! John

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Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast
by Antonin Skoch 02 May '17

02 May '17

Doug, did you process from scratch or did you retain edits to brainmask.mgz and wm.mgz? The -cubic should not be necessary, since recon-all (which I primarily obtained from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ has UseCubic=1 ). I could try to replicate v5.3 again on my side. Antonin It is subject #1, trying to replicate in our version of 5.3 using the scripts/recon-all.local-copy ./recon-all.local-copy -all -FLAIRpial -s 1.dng.v53.local-cubic -cubicThe results were close, but they were not exact On 5/1/17 4:13 PM, Antonin Skoch wrote: Dear Doug, that is strange. What precisely you cannot replicate? The results with v5.3 or with v6.0? What subject from the group I uploaded you have tried? I could try to run the comparison again but I have seen the results already in many subjects and the difference between -cubic and no cubic seems profound and systematic in favor of v5.3 in the aspect of wm.mgz leak ouside brain and GM/WM contrast. Concerning the expert options file: Despite using flag -xopts-use in recon-all in v5.3, I did not use any expert option file in the subject I have uploaded. The reason of using -xopts-use was that I was processing the subjects in batch where some of them had expert-options file with entry bbregister -init-header due to the fact that init-fsl failed in these subjects. I wanted to make my life easier by processing all of them by identical recon-all command line parameters and added -xopts-use to all subjects (even in the subjects without expert option file). I supposed that this could not do any harm. Antonin I can't seem to replicate your results locally, even with the recon-all you used. The one thing I'm missing is the expert options file. Can you send that to me? On 04/24/2017 12:49 PM, Antonin Skoch wrote: > Dear Doug, > > the subject with leak of white surface outside brain (my first post with > screenshots) is subject 1. Slice number (coronal) around 100. > The subject in second post (with text below) is subject 2, slice number > (coronal) also 100. > > I have processed the subjects with v 6.0 (in fact dev version from feb 2017, > but this is irrelevant) with -cubic -no-mprage. It looks much like v5.3, i.e. > the wm.mgz and surfaces are much better, but v5.3 looks still better, at > least for subject 1. > I have uploaded them as file v6.0_cubic_no_mprage.tar.gz to your ftp site. > > The optical difference in norm.mgz/brain.mgz between v5.3 and v6.0 with > -cubic is very minor, but still there is some other thing which renders > wm.mgz worse than with v5.3 for subject 1. > The -cubic has profound effect, the images seem much smooth with lose of > contrast without using -cubic. > > Regards, > > Antonin > > > And what slice number? > On 04/24/2017 11:16 AM, Douglas N Greve wrote: > > Anonin, of the three subjects you sent, which one is shown in these > > pictures? > > > > > > On 04/19/2017 05:23 PM, Antonin Skoch wrote: > >> Dear experts, > >> > >> I am sending just one more example to illustrate issue with white > >> surface estimation in v6.0. See the attached screenshots: In v6.0 > >> there seems to be insufficient contrast in brain.finalsurfs.mgz, so > >> the white surface is leaking at three spots dramatically outwards > >> towards pial surface. The white surface in v5.3 looks much more > >> anatomically relevant in the same spot. > >> > >> Could you please comment on how to avoid such issues in v.6.0? > >> > >> Regards, > >> > >> Antonin Skoch

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Re: [Freesurfer] perform group analysis on user defined maps
by Ladan Shahshahani 02 May '17

02 May '17

Hi Douglas, Thanks for the reply. One more question, Qdec excludes subjects with NaN values, right? How will mri_glmfit treat subjects with NaNs? For each subject, there are some vertices with NaN values (These vertices are not the same in all subjects). Bests, Ladan

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Freesurfer May 2017