Re: [Freesurfer] converting ME-MPRAGE files

We ran the following command, but the clarity improved minimally. Therefore, is there another command that you would recommend. Thanks, Gaurang On 6/9/16, 5:30 PM, "Douglas N Greve" wrote: >That tells you there is one "series" in that folder. The series here

[Freesurfer] BERT is not working correctly with the toolbox list below the brain

  When I open freesurfer and type the command to pull up bert the brain pops up but the toolbox (icons) below it that are supposed to come up as well do not? Help is appreciated! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Freesurfer Help

Hello, I just downloaded and installed Freesurfer and I had just a few basic questions.  1. When I type in the command to "test the installation type" using "tksurfer bert lh inflated -annotation aparc" I get the bert brain image, however I don't get the tksurfer tools popup below it with all

Re: [Freesurfer] using both T1/T2 and resolutions

I'm interested in getting both the most accurate cortical surfaces and volumetrics. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: Friday, June 10, 2016 12:54 PM To: Freesurfer support list

Re: [Freesurfer] using both T1/T2 and resolutions

Oh gosh, you’re right Matt. Sorry about this! Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 10 Jun 2016, at 18:54, Matt Glasser > wrote: Hi Eugenio, I think he is

Re: [Freesurfer] using both T1/T2 and resolutions

Hi Eugenio, I think he is just after cortical surfaces. Matt. From: on behalf of "Iglesias, Eugenio" Reply-To: Freesurfer support list Date: Friday, June 10, 2016 at 12:30 PM To: Freesurfer

Re: [Freesurfer] using both T1/T2 and resolutions

Hi! I actually sent out an email yesterday regarding this. The way that the subfield module is set up, you cannot take advantage of your full res T1 and your T1. We are working on a solution. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London

Re: [Freesurfer] Brainstem Substructures does not work.

FreeSurfer 6.0 is not available yet, but you can download the development version to take advantage of this functionality. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 10 Jun 2016, at

[Freesurfer] Brainstem Substructures does not work.

Dear FSL expert: Firstly, I would like to thank for the reply from Douglas. Thank you for your suggestion! aparcstats2table is working!. Then, I have another question about the brainstem substructures. According to the guideline, https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime I download

Re: [Freesurfer] selxavg3-sess error

Hi Doug, it looks like my email with attached the Xtmp.mat file didn't arrive. How can I send it to you? Thanks! Francesca 2016-06-08 15:44 GMT+02:00 Douglas Greve : > Do you have both polar and eccen data? If so, can you send the Xtmp.mat > file? > > > On 6/8/16 6:08

Re: [Freesurfer] using both T1/T2 and resolutions

Hi Jim, I would just use the HCP Pipelines for that: https://github.com/Washington-University/Pipelines, as they take care of all of those things re FreeSurfer. I would set to using the 0.8mm templates so that nothing is down sampled. Peace, Matt. From:

[Freesurfer] Intensity normalization issues leading to improper segmentation

Dear Freesurfer list, Maybe I am hoping for a miracle with my question, but I am bit desperate after unsuccessfully trying things around for over a year. In a nutshell, I need advice on the intensity normalization options. We have T1 data from twins (8-25years) acquired on a 3T MR750 GE scanner

[Freesurfer] Remove zeroes from mri_segstats in mean calculation?

Hello, I am running mri_segstats to get the intensity mean of a custom image volume, but I do not want zeroes to be included in the calculation of the mean. Is there an option to remove zeroes from this calculation or another potential workaround? Thanks very much! Bimal

[Freesurfer] using both T1/T2 and resolutions

Hi, We'd like to process pediatric data through the complete FS 5.3 pipeline. The T1/T2 data are acquired with a 3T Siemens as follows: T1 mpr sag - 0.82x0.82x0.85 T2 Space - 1x1x1 We'd like to process using both the T1 and T2 (for better dura removal and possible myelin analysis). Is it

Re: [Freesurfer] Symmetric label on fsaverage

Quick update on my situation: it turns out that I have a problem corresponding to the source label: ERROR: Option --src-label unknown Thanks in advance for your help :) 2016-06-09 20:08 GMT+02:00 Alexandre Routier : > Hello, > > Sorry for my late reply but I just

Re: [Freesurfer] Cerebellar volumes?

Hello, This paper is very relevant to this issue: Sanfilipo MP, Benedict RH, Zivadinov R, Bakshi R (2004) Correction for intracranial volume in analysis of whole brain atrophy in multiple sclerosis: the proportion vs. residual method. Neuroimage 22:1732–1743. Anthony On 6/10/16 9:34 AM,

Re: [Freesurfer] Cerebellar volumes?

Hi Bruce, No, I expect cerebellar volume to vary with diagnosis, but I want to account for the head size differences. This seemed to me the way to do that, but of course I am not an expert. Best, Marja On Fri, Jun 10, 2016 at 11:23 PM, Bruce Fischl wrote: > if you

Re: [Freesurfer] Cerebellar volumes?

yes, but you would expect uninteresting variance with head/intracranial vault size, which is why you would include it as a regressor On Fri, 10 Jun 2016, Marja Caverlé wrote: Hi Bruce, No, I expect cerebellar volume to vary with diagnosis, but I want to account for the head size differences.

Re: [Freesurfer] Cerebellar volumes?

if you expect cerebellar volume to vary in an uninteresting way with head size (which I think you probably do) On Fri, 10 Jun 2016, Marja Caverlé wrote: Ok Thanks! Just to be sure, the eTIV would also make the cerebellar numbers more informative right? Best, Marja On Fri, Jun 10, 2016 at

Re: [Freesurfer] Cerebellar volumes?

Ok Thanks! Just to be sure, the eTIV would also make the cerebellar numbers more informative right? Best, Marja On Fri, Jun 10, 2016 at 11:14 PM, Bruce Fischl wrote: > Hi Marja > > yes, you can just use those volumes, and no, including it as a regressor > isn't the

Re: [Freesurfer] Cerebellar volumes?

Hi Marja yes, you can just use those volumes, and no, including it as a regressor isn't the same as dividing by eTIV (although you can do that instead). cheers Bruce On Fri, 10 Jun 2016, Marja Caverlé wrote: Ok thanks Bruce. If I want to use these cerebellar white matter volumes, I

[Freesurfer] Combining cross sectional and longitudinal analyses

Hi I have two groups I want to compare, in total 172 scans Of these 78 got a a follow up. Groups are approximately evenly distributed. I want to do first a cross sectional comparison and subsequently a longitudinal analysis for the 78 subjects only. My question is: (1) Is it is valid to

Re: [Freesurfer] Cerebellar volumes?

Ok thanks Bruce. If I want to use these cerebellar white matter volumes, I assume I also need to use the eTIV as regressor right? (just like for the cerebral volumes? And maybe a stupid question, but can I use the eTIV as regressor by just dividing the structure volume by the eTIV? Best, Marja

Re: [Freesurfer] Cerebellar volumes?

Hi Marja we do whole cerebellum white matter and gray matter, but things like lobules aren't released yet. cheers Bruce On Fri, 10 Jun 2016, Marja Caverlé wrote: Hi all, I am hoping to find some cerebellar volumes, but I don't know how to get them. I already did recon -all on all my

[Freesurfer] Cerebellar volumes?

Hi all, I am hoping to find some cerebellar volumes, but I don't know how to get them. I already did recon -all on all my subjects, but I cannot find any of these numbers in the .stats files. Am I just missing them, or does the recon all not do any cerebellar stuff? Best, Marja

[Freesurfer] GLM: Define the design matrix by myself

Hello, Freesurfer experts: I want to define the design matrix by myself in GLM, I know that in FS, when we deal with the categorized factors, we treat them as classes, So basically, I want to make a design matrix like this: 1) formula_EffectOnGroupWithAgeGenderCovariates = 1 + TermGroup +

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Matt, Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t crash when you run it! That said, I need to go through the code, and make sure that data are handled the way they are supposed to: the fact that it doesn’t crash doesn’t directly imply that it is working