[Freesurfer] Convert label file to STL file‏

Dear Freesurfer Experts, I'm trying to convert .label file to .stl file. In more detail of my purpose, I want to get separate stl files of whole brain. Now, I want to make stl files of label files which made from ?h.aparc.a2009s.annot. First, I tried to convert lh.pial to lh.pial.stl, I've

[Freesurfer] Research position at Columbia University Medical Center {Disarmed}

The Molecular Imaging and Neuropathology Division at Columbia University Medical Center is seeking a full-time image analyst to begin working immediately. The position involves assisting in the processing of brain imaging data, including positron emission tomography (PET) and structural and

Re: [Freesurfer] Group analysis tutorial

Hi Qijing, Under the 'Freeview dev build' section on this wiki page you can download an updated version of freeview. http://freesurfer.net/fswiki/Download -Louis On Mon, 7 Jul 2014, Qijing Yu wrote: Hi Doug, By new version, do you mean v5.3.0? Qijing On Mon, Jul 7, 2014 at 11:31

Re: [Freesurfer] bad freesurfer segmentation

Hi Bruce, Thanks for your reply. In my previous e-mail I already tried to attach one of my subjects, but got the response that the message was too big, and therefore it was rejected. So how should I upload the image? The images are T1-weighted, 3D, acquired with a 3T scanner, resolution 256

Re: [Freesurfer] Convert label file to STL file‏

It probably thinks the STL file is just a mesh without coloring. Peace, Matt. From: Mat yuki matsuyuki2...@outlook.jp Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, July 10, 2014 at 7:19 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] bad freesurfer segmentation

Hi Doety, Consider these options for uploading data: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html I think recon-all is expecting your wm.mgz to be conformed or 256^3. Something like: mri_convert wm.mgz wm.conform.mgz

Re: [Freesurfer] combining aseg and seg_edited files for an atlas

If you have matlab, it would be pretty easy to do it there, something like aseg = MRIread('aseg.mgz'); seg = MRIread('seg_edited.mgz'); % Your first seg inside cerebellum indseg1 = find(seg.vol == 1 (aseg.vol == 8 | aseg.vol == 47)); % cerebellum cortex = 8 and 47, see

Re: [Freesurfer] Compiling data from lobesStrict

I don't think you need to do steps 2 and 3. Just run mri_annotomical_stats on the lobes annot just like it is done for aparc. Look in the recon-all.log file for the command line doug On 07/08/2014 02:42 PM, krista kelly wrote: Hi all, I'm trying to extract cortical thickness data from each

Re: [Freesurfer] input anatomy orientation

This is expected, unfortunately. When you change the orientation, it changes the interpolation which changes things slightly. Those areas are all pretty small so the changes can appear to be large (though they are only a few percent). doug On 07/09/2014 01:42 PM, Kathy L. Pearson wrote: I

Re: [Freesurfer] Categorical covariates with more than two levels on qdec

You cannot use qdec for this. You must use the command line stream. There is a tutorial for this as well as a presentation on our wiki. Basically, you will need to create your FSGD file, run mris_preproc, mri_surf2surf to smooth, mri_glmfit, and mri_glmfit-sim doug On 07/09/2014 03:43 AM,

Re: [Freesurfer] Jacobian mri_cvs_register

Hi Andre You can run: mri_jacobian -tm3d 3d morph template volume output volume --Lilla On Thu, 10 Jul 2014, André Ribeiro wrote: Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis?

[Freesurfer] Jacobian mri_cvs_register

Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? Regards, Andre Santos Ribeiro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Group analysis tutorial

Thank you Doug and Louis!! was stuck in something else in the past few days. I will try the new version and let you know if I still have problems viewing the results. Thanks again! Really appreciate your help! On Thu, Jul 10, 2014 at 10:57 AM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu

Re: [Freesurfer] combining aseg and seg_edited files for an atlas

Thank you Douglas for the suggestion, I will try this method! Alexarae On Thu, Jul 10, 2014 at 11:43 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: If you have matlab, it would be pretty easy to do it there, something like aseg = MRIread('aseg.mgz'); seg =

[Freesurfer] Question about LGI

Hi FS Community, I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume. Thanks in advance, Panos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Question about LGI

Hi Panos, It all depends on what your question is: whether the between-group difference in LGI and surface area is an absolute difference (then don't correct), or whether you want to see if it holds after correction. In any case, by geometric definition, the relationship between surface area,

Re: [Freesurfer] Question about LGI

Hi Marie, Thank you for your reply. I wanted to compare the LGI and Surface Area between two cohorts, from which one has a significantly higher intracranial volume than the other. I was wondering about the correction because the results, especially in the case of SA, are the opposite before and

[Freesurfer] Understanding Hippocampal volume stats

Hi, Freesurfer reported the following hippocampal volumes for a subject volumeInVoxels: right_CA1: 2652.3 right_CA2_3: 7245.11 right_CA4_DG: 3967.28 right_fimbria: 423.555 right_hippocampal_fissure: 191.897 right_presubiculum: 3598.99 right_subiculum: 4868.1

[Freesurfer] Tracula

Hello, I have a few questions about Tracula. I am very new to DTI, so I hope you can bare with me. 1.) I have been checking my registration at the prep stage. I am very new to this so it may be that I am not looking at the right files. I looked at my eddy current corrected diffusion data

Re: [Freesurfer] Question about LGI

Hi Panos, Then I would say that it's interesting to understand why the results change depending on the correction. Here is a list of papers that may be relevant, but you'll certainly find many others: http://www.ncbi.nlm.nih.gov/pubmed/8159014 http://pages.jh.edu/~kechen/pnas-brains.pdf

Re: [Freesurfer] Question about LGI

For surface area, you should correct with the ICV (note you should use ICV and not something like ICV^(2/3)) doug On 07/10/2014 04:52 PM, Marie Schaer wrote: Hi Panos, Then I would say that it's interesting to understand why the results change depending on the correction. Here is a list

[Freesurfer] ACPC alignment in freeview?

Hello Freesurfer experts: I am wondering if I can do ACPC alignment in freeview. Perhaps using Tools Transform volume and then rotating using landmarks. Is this indeed possible? If so, can anyone provide guidance on the 3 landmarks to select (would it be anterior commissure superior posterior

Re: [Freesurfer] Convert label file to STL file‏

Hi Matt, Thank you for your reply. It is impossible to convert label file to stl file, is it wright? If it was so, do you know how to get it? I want to get stl files which divided into each percellation, if its possible. Thanks in advance, Yuki. Date: Thu, 10 Jul 2014 10:25:19 -0500 From: