[Freesurfer] Different Sequences Longitudinal Stream {Disarmed}

? Thank you very much, kind regards! Lea Backhausen -- Lea Backhausen Ph.D. Student (M.Sc. Psychology/Neuroscience) Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://secure-web.cisco.com

[Freesurfer] local gyrification index unit

External Email - Use Caution Hi FreeSurfer experts, I have recently been wondering about the correct unit for curvature and local gyrification index. For curvature I find inconsistent information like: mm^-2 (https://onlinelibrary.wiley.com/doi/epdf/10.1002/ima.20138, page 47),

Re: [Freesurfer] Direction of significant group comparison

/100408.far/lhsurf.mgh ? --out > $out/preproc_FP_cf_lh/lh.paired-diff.FP_cf.mgh --f $sublist > --paired-diff > > *The output log shows no errors, the number of inputs equals the > number in the subject list and it creates a file but it?s all zeros. I > just have no idea as to why t

[Freesurfer] Direction of significant group comparison

External Email - Use Caution Dear FreeSurfer experts, I am running whole-brain based group comparisons of cortical measures between a patient group and a control group using glm-fit and Monte-Carlo correction for multiple comparisons. It works fine but I am not sure where to

Re: [Freesurfer] ERROR: dimension mismatch between X and

10 values, thus the error. On 09/27/2018 09:39 AM, Backhausen, Lea wrote: > > External Email - Use Caution > > Dear FreeSurfer experts, > > I get this error message when running group analysis on cortical > thickness using glmfit: > ERROR: dimension mismatch betwee

[Freesurfer] ERROR: dimension mismatch between X and contrast

External Email - Use Caution Dear FreeSurfer experts, I get this error message when running group analysis on cortical thickness using glmfit: ERROR: dimension mismatch between X and contrast Contrasts/ADHD_COM_TD_age_IQ.mtx X has 9 cols, C has 10 cols Please find attached the

Re: [Freesurfer] Euler number as quantitative quality measure

ated Manifold Surgery paper if you are interested in the details) cheers Bruce On Thu, 12 Jul 2018, Backhausen, Lea wrote: > > External Email - Use Caution > > Hey Freesurfer Experts, > > I would like to use the Euler number as a quantitative quality m

[Freesurfer] Euler number as quantitative quality measure

External Email - Use Caution Hey Freesurfer Experts, I would like to use the Euler number as a quantitative quality measure of my reconstructed data as Rosen et al. (2017) recommend in their recently published paper.

Re: [Freesurfer] glmfit-sim FWHM 34?

e to use permutation rather than monte-carlo-based correction. On 07/03/2018 11:40 AM, Backhausen, Lea wrote: > > > Dear FreeSurfer experts, > > I am trying to do vertex-wise comparisons for thickness, surface area > and volume between three groups with glmfit.

[Freesurfer] glmfit-sim FWHM 34?

External Email - Use Caution Dear FreeSurfer experts, I am trying to do vertex-wise comparisons for thickness, surface area and volume between three groups with glmfit. Currently I am using the dev version ( freesurfer-darwin-OSX-ElCapitan-dev-20180627-4a8f901 )

[Freesurfer] Prospective motion correction sequences

External Email - Use Caution Dear FreeSurer experts, has anyone of you ever used prospective motion correction techniques like PROMO or BLADE/PROPELLER? We are planning a new study with children and adolescents with obsessive-compulsive disorder and thought about implementing

[Freesurfer] FW: Number of iterations with --cache flag

CWP<.05 or is the CWP less important when using stricter thresholds? 4) Which surface area do you use in your paper? White or pial? Is one "better" to use than the other? Thank you so much for your input! Best, Lea Backhausen ------ Lea Backhausen Re

[Freesurfer] FW: Number of iterations with --cache flag

External Email - Use Caution Sorry, found it! It’s 1 as indicated in the sig.cluster.summary file. Best, Lea Backhausen -- Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden

[Freesurfer] Number of iterations with --cache flag

to the right page? Thank you for your help! Best Lea Backhausen -- Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden

Re: [Freesurfer] SLURM - speed processing (Alexandre Obert)

External Email - Use Caution Hi Alex, I am also running FreeSurfer 6.0.0 on SLURM and recently did some tests on how to parallelize it, how much ressources to ask for… This is what I learned: 1) FreeSurfer 6.0.0 is able to use OpenMP parallelization (I guess for the

[Freesurfer] 3T flag recon-all

Hi all, Would you recommend using the 3t flag for recon-all when analyzing data from a 3t scanner? I read about it in some papers but not everybody seems to use it. Also, do you know whether the flag can be used in the longitudinal stream as well or does it only apply to the crosssectional

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} (Martin Reuter)

Hi Martin, thank you so much for your detailed answer. I will see how we can implement these modifications. Just two quick follow up questions: 1) I have half of the data already processed with the CROSS step using FS 5.3.0. Is it possible to use this data when running the TEMPLATE and LONG

[Freesurfer] Longitudinal analysis using SLURM {Disarmed}

Dear FS experts, I am trying to do a longitudinal analysis of around 250 adolescents with up to 4 data points each. Given the complexity I would like to use the long_submit_jobs script which is described here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts Unfourtunately it does

[Freesurfer] Group and ROI analyses in qdec

Dear freesurfer experts, I started using qdec for comparing cortical measures in adolescent patients with ADHD versus typically developing adolescents and I have a few questions concerning the ROI analysis as well as the Desikan-Killiany versus Destrieux atlas. English is not my native