Freesurfer

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30132 discussions

CentOS 7 and freeview
by Ly, Kien-Ninh Ina,M.D. 03 May '17

03 May '17

Hi Freesurfer experts, I installed CentOS 7 on my computer and tried running freeview in the terminal window after ssh’ing into a remote computer. The software opened up correctly and I was able to see the toolbars; however, the main screen where the images should be showed a distorted background. Has anyone encountered this problem before? Is there anything I need to install before running freeview? When I previously ssh’ed into the same remote computer using Mac OS Sierra, freeview worked perfectly fine. Many thanks for your help. Best, Ina

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Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files
by Salil Soman 03 May '17

03 May '17

Thank you for your email. Just to follow up, the rh and lh hippocampal hippoSfVolumes-T1.v10.txt files are present, but for a large number of cases, only the lh hippoSfVolumes-T1.long.v10.txt files are present. I reran the exact same recon-all -long command for all the cases, and I reran them after your suggestion, but there is no change in the number of missing rh.hippoSfVolumes-T1.long.v10.txt files. The log file for the longitudinal processing for recon-all says the process completed with no errors. Is there anything else I should check? Thanks! On Fri, Apr 14, 2017 at 3:54 AM Alan Francis <alandarkenergy(a)gmail.com> wrote: > Hi Salil: > > It could be that the HSF script may have `errored out' mid way through the > analysis. If you go through the recon processing steps which are one of the > output files, you will see exactly where the error occurred. Just reprocess > that brain and see if that happens again. > > Hope this helps, > > best, > > Alan > > > > On Thu, Apr 13, 2017 at 4:49 PM, Salil Soman <sal(a)jhu.edu> wrote: > >> Hi, >> >> I have run a number of cases through the FS6 hippocampal longitudinal >> processing steps listed at https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields >> and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing >> >> It seems that all steps completed, but when it came time to collect the >> results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67) >> than rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what >> I may be doing incorrectly? >> >> Thanks! >> >> Salil Soman >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > *Alan N. Francis PhD* > Regional Sales Manager/ Application specialist > Nordic Neurolab > Boston. > alan(a)nordicneurolab.com > > > *Previously:* > Instructor - Imaging Neuroscience > Brain Imaging Center > McLean Hospital > Harvard Medical School > 115 Mill Street, Belmont, MA 02478 > alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> > afrancis(a)mclean.harvard.edu > > > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| >

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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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