[Freesurfer] Postdoctoral Fellow in Multivariate Analysis, Machine Learning and Classification

Job description: Computation functional anatomy laboratory at National University of Singapore focuses on the development of medical image analysis methods, including image segmentation, registration approaches, multivariate statistical analysis, machine learning, and classification algorithms. Our

[Freesurfer] Postdoctoral Fellow Position on High Angular Resolution Diffusion Imaging

Job description: National University of Singapore (NUS) is a leading global university centre in Asia. It offers a global approach to education and research, with a focus on Asian perspectives and expertise. Computation functional anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa) focuses

[Freesurfer] Postdoctoral Fellow in Multivariate Analysis, Machine Learning and Classification

Job description: Computation functional anatomy laboratory at National University of Singapore focuses on the development of medical image analysis methods, including image segmentation, registration approaches, multivariate statistical analysis, machine learning, and classification algorithms. Our

[Freesurfer] Dealing with missing clinical variables in lme analysis and test model fit between two models with the same number of random effects.

Dear FreeSurfer experts, In my dataset, I am missing some of the clinical variable for some of the subjects. How do I represent missing variables to the linear mixed model? Should I use zero or use the mean? It is possible to test the model fit of intercept compared to time with lme_mass_LR. B

Re: [Freesurfer] bblabel

I looked more into label files and coordinate systems, and finally I think I found the reasons why bblabel did not work. Here they are: 1. The example in bblabel is wrong, because the bounding box points to the right hemisphere (xmin>0), that's why it returns a file with no vertices (the file c

Re: [Freesurfer] Fwd: Jacobian mri_cvs_register

Hi Andre, The jacobian field is computed in the coordinate space of the moving volume so if you overlay it with brain_IBSR_01.mgz, you will see that they match. We currently do not have an executbale in 5.3 that writes out the m3z transforms in nifti format. Lilla On Tue, 5 Aug 2014, And

Re: [Freesurfer] Fwd: Jacobian mri_cvs_register

Hi Lilla, Thank you for your response. I would argue that they seem to be aligned, yet they are not. If you look at the cerebellum the Jacobian is shifted in respect to the brain_IBSR_01.mgz. Further, there must be a jacobian for each voxel of the brain_IBSR_01.mgz (at least inside the brain mask)

Re: [Freesurfer] Fwd: Jacobian mri_cvs_register

Hi Andre, I would argue that they seem to be aligned, yet they are not. If you look at the cerebellum the Jacobian is shifted in respect to the brain_IBSR_01.mgz. Further, there must be a jacobian for each voxel of the brain_IBSR_01.mgz (at least inside the brain mask), which does not happen

Re: [Freesurfer] occipital lobe WM errors

Hey Bruce, Thanks so much. If it would help, I could upload another subject, perhaps one with worse segmentation in the occipital lobe. I could also upload a raw T1 image sequence (Nifiti) Matt On Wed, Aug 6, 2014 at 9:48 AM, Tirrell, Lee wrote: > Hi Matt, > > I've taken a look at the subjec

[Freesurfer] Available post doc position

At the Research Group for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have an available post doc position for an excellent candidate, on the project Inflammation, Amyloid and Atrophy in the Aging Brain: The Borders between Healthy Brain Aging and Neurodegeneration.

[Freesurfer] Recon-all Error

Hello, I am extremely new FreeSurfer user, and have hit a bump in the road while trying to run -autorecon1 and -autorecon2. The process seemed to be running smoothly until I got the following warning messages for every file number, and then it was randomly killed- * WARNING: TP 890 to 1 did not c

Re: [Freesurfer] Recon-all Error

Hi Esha what are you trying to do? From this output it looks like you are runing a ~1000 time point longiutdinal study, which I assume is not what you meant. Please be sure to include the exact command you ran! cheers Bruce On Wed, 6 Aug 2014, Esha Mehta wrote: Hello,  I am extremely ne

[Freesurfer] tracula longitudinal

Getting ready to run longitudinal tracula. Does the sublist entries in the dmrirc.long file refer to the cross-sectional or longitudinal processed subject time points? set subjlist = ( huey-scan1 \ huey-scan2 \ dewey-scan1 \ dewey-scan2 \

Re: [Freesurfer] Recon-all Error

Hi Bruce, The exact command I ran was recon-all -autorecon1 -autorecon2 -subjid DNS_highRes_N892 I do have ~1000 scans, but it is not a longitudinal study. They are located under the DNS_highRes_n892/mri/orig/ directory in the .mgz format. Let me know if you need anymore information. Thanks!

[Freesurfer] mpr2mni305 failed error

I all! I am a new freesurfer user. I have a problem when I perform the recon-all -all, in about 15% of MRI scans, all made with the same scanning protocol (T1 MPRAGE in a SIEMENS Avanto 1,5 T). I can't recognize any difference between those scans which work correctly and those not. I have never f

Re: [Freesurfer] Recon-all Error

can you send us the complete screen output of your command and also the recon-all.log? thanks Bruce On Wed, 6 Aug 2014, Esha Mehta wrote: Hi Bruce,  The exact command I ran was  recon-all -autorecon1 -autorecon2 -subjid DNS_highRes_N892 I do have ~1000 scans, but it is not a longitudinal

Re: [Freesurfer] mri_cor2label: volume --> .label vectors

On 08/06/2014 11:40 AM, Krieger, Donald N. wrote: > > mri_cor2label does work for extracting vectors with > FreesurferColorLUT.txt label numbers from .mgz volumes. > > The documentation at > http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2label >

Re: [Freesurfer] Interpreting clusters 'holistically' vs in terms of max coordinates

I would definitely show a picture of it, say which areas it overlaps, and spec the coordinates for the max (which is what QDEC reports). doug On 08/05/2014 06:39 PM, Francesco Puccettone wrote: > Hello, > > If a QDEC analysis returns a certain cluster as being significantly > different between

Re: [Freesurfer] label to surf (.mgh file)

Hi Sara, I'm not sure what you are trying to do. Are you doing a volume or surface-based analysis? If surface based, why do you need to convert it into the volume? doug On 08/05/2014 11:48 PM, Sarah Whittle wrote: > Hi, > > I would like to create an overlay from a number of labels from the sta

Re: [Freesurfer] bblabel

You are correct. The problem is actually that the echo commands sees the question marks and interprets them as wildcards (like *) for file names, but it cannot find such files and it it dies. I've attached a new mri_mergelabels script which should fix the problem. Copy it to $FREESURFER_HOME/

Re: [Freesurfer] tksurfer tool "graph marked vertices avg" not active

what tutorial are you looking at? On 08/04/2014 12:59 PM, Katharina Zech wrote: > Dear all, > > I have a problem regarding tksurfer ROI cluster extraction after full > mc-simulation: I marked my cluster of interest as described in the > freesurfer tutorial. But when I choose Tools --> Group, "G

Re: [Freesurfer] FW: YANQ follow-up

How did you create that image? You can use mri_cor2label to extract the labels from aparc+aseg (it will take values > 255) doug On 08/04/2014 01:16 PM, Krieger, Donald N. wrote: > > Thanks Doug, > > Got it. > > I've attached a sample image on which I've drawn transformed vectors from: > > 1.rh.

[Freesurfer] FsFast Functional Connectivity Analysis

Hi Doug, I was trying to run functional connectivity analysis following instructions on the FreeSurferWiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough). I was able to successfully run the following commands (nothing errored as far as I can tell) but the resul

Re: [Freesurfer] FsFast Functional Connectivity Analysis

When you say that they are "empty" what do you mean? That there is nothing above threshold or that there is nothing regardless of how low the threshold is? See if you get something if you set the thresh close to 0. Does this happen in the volume and the surface? Have you checked the registrati

Re: [Freesurfer] Post-hoc test failure by ROI extraction after successful group analysis with FreeSurfer

Two things. First, I would extract the data straight from the stack used as input (--y) to glmfit instead of mapping the label back to each individual. There are a number of transformation that are hard to make symmetrical going from subject to fsaverage and back. This can particularly affect

Re: [Freesurfer] mpr2mni305 failed error

Try it with -notal-check doug On 08/06/2014 04:39 PM, Francesco Deleo wrote: > I all! > > I am a new freesurfer user. > I have a problem when I perform the recon-all -all, in about 15% of > MRI scans, all made with the same scanning protocol (T1 MPRAGE in a > SIEMENS Avanto 1,5 T). > > I can't r

Re: [Freesurfer] license file not working

Hi Philipp, is this still a problem? If so, can you send me your license file. I've gone off-list because I don't want the license files posted to the list. doug On 08/01/2014 04:22 PM, Saemann Philipp wrote: > Hello Douglas, > > the file created on Linux, no Windows involved, and was 100% iden