[Freesurfer] Opening positions

Opening positions (postdoc, research assistant, or professorship) for collaborative projects from the Center for Human Brain Research, Hangzhou Normal University (Professor WENG Xuchu, wen...@psych.ac.cn), Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University (Professor Z

[Freesurfer] position ad for image analysis

A full-time position as image analysis specialist is available at the Section of Biomedical Image Analysis (SBIA), of the Department of Radiology, University of Pennsylvania. The successful candidate must have a Bachelor's or Master's degree in Electrical or Biomedical Engineering, or Computer

[Freesurfer] Blocked Design

Hello, We are attempting to run an analysis using selxavg3-sess but keep getting an error. We are using: freesurfer v5 Our subjects directory: /cluster/manoach/milton/subjects Command that was run: selxavg3-sess -analysis mandylh2 -fwhm -s PAMST06 Output that was given: Creating Design Matr

Re: [Freesurfer] DCM filename problems with recon-all

It's having a problem with something in the header of the file. Try using mri_convert directly and specify that this is a GE dicom (see mri_convert -help). doug Joakim Vinberg wrote: > > Hi everybody, > > I have several older anatomical series that I would like to run > through recon-all. Unfo

[Freesurfer] DCM filename problems with recon-all

Hi everybody, I have several older anatomical series that I would like to run through recon-all. Unfortunately, the DCM files were pulled down with an older filename convention that seems to trip mri_convert immediately, and I'm having some trouble interpreting the error. Can anybody shed any

Re: [Freesurfer] retinotopy manual?

I don't have a formal manual yet (working on it). Below are a list of steps that you need to run. The version 5 retinotopy stream is now integrated with the rest of FSFAST, which is documented here: http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt doug 1. Create retinotopy paradigm file in e

Re: [Freesurfer] Memory allocation problem with mri_robust_template

To Martin, Thanks a bunch. I haven't tested out all the recommendations, but at least I know what's going on. If I did want to convert to uchar, how would I go about this? Is there a function included in the Freesurfer package, or would I have to write my own function to do so? It's not a concern,

Re: [Freesurfer] confusion about look up table labels...

gyrus and sulcus cheers Bruce On Fri, 11 Feb 2011, Joe Andreano wrote: > Hi, > > I'm looking at the list of anatomical regions (found here: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT) > and I notice that there are two separate sets of coordinates in t

[Freesurfer] confusion about look up table labels...

Hi, I'm looking at the list of anatomical regions (found here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT) and I notice that there are two separate sets of coordinates in the same hemisphere for rostral ACC: 1201, G_cingulate-rostral_ACC, and 1206, S_cingu

Re: [Freesurfer] mapping surface vertices to functional voxels

Sorry, this should be: M = inv(Ta)*inv(R)*Tf doug Douglas N Greve wrote: > Hi Jim, I can't quite follow all of that. To go from a functional CRS > to an anatomical CRS, you'd need > > M = Ta*inv(R)*Tf > where Ta is the vox2raatkr for the anat > Tf is that of the func > and R is the register.da

Re: [Freesurfer] Segmentation into native space

Hi Yolanda, that looks correct, though you might want to use mri_label2vol instead of mri_vol2vol. mri_label2vol will handle certain cases better (like when multiple conformed voxels land in a single rawavg voxel). But why do you need to go to rawavg space anyway? If you're going to just count

Re: [Freesurfer] Projecting findings using Freesurfer

Hi Brian, I can't quite figure out what it is you are trying to do. What do you mean by "project"? Project onto what? And by volumes do you mean the structure volumes (like the hippocampus) or surface volumes? doug Weisinger, Brian (NIH/NIMH) [F] wrote: > Good Morning, > > I am attempting to pro

Re: [Freesurfer] mapping surface vertices to functional voxels

Hi Jim, I can't quite follow all of that. To go from a functional CRS to an anatomical CRS, you'd need M = Ta*inv(R)*Tf where Ta is the vox2raatkr for the anat Tf is that of the func and R is the register.dat mtx I would compare what you get to mri_vol2surf output. If they match, then you're go

Re: [Freesurfer] Contrasts for GLM DODS with both discrete as continues covariates

Hi Petra, you have mixed up a class with the level of a factor (an easy thing to do). From your FSGD, it looks like you would need 8 classes, each class would be a combination of a level from each factor. So one class would be control-male-adni, etc. Once you have a proper FSGD file, FreeSurfer

Re: [Freesurfer] Segmentation into native space

Thank you Bruce! I would like to segment a set of caudates into head and body and then obtain the real volume of these two parts. The procedure that I am applying is the following: 1.- Applying the standard recon-all process 2.- Extracting the "conformed" voxel geometry caudate with the following

[Freesurfer] Projecting findings using Freesurfer

Good Morning, I am attempting to project R squared values that were calculated using Freesurfer volumes for the various automated segmented areas that are calculated in Freesurfer. Is there a way I can can compare two groups in say QDEC and visually see the results? Thank you for your help.

[Freesurfer] Contrasts for GLM DODS with both discrete as continues covariates

I want to run a GLM DODS in Freesurfer to test whether patients differ from controls with regard to cortical thickness, meanwhile I want to control for several variables, both discrete as continues. This is my manually made fsgd file GroupDescriptorFile 1 Title fsgd pat con.txt MeasurementN