Re: [Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask

External Email - Use Caution Hi Bruce, Sorry for the late reply. I have been searching the forum and the freesurfer wiki. Are there instructions somewhere on how to do this in matlab? Thanks, Lindsay On Thu, Dec 20, 2018 at 2:41 PM lindsay hanford wrote: > Hello Freesurfer Commu

Re: [Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask

Hi Lindsay you can use the m-file read_curv.m to read in the thickness file (lh.thickness or rh.thickness). You can also load .mgf files with either load_mgh.m or MRIread.m, then compute the mean in any subset of the vertices you want. cheers Bruce On Fri, 4 Jan 2019, lindsay hanford wrote

[Freesurfer] Job Opportunity

External Email - Use Caution Good Day I would like to extend a job opportunity at the University of Texas at Dallas. Please forward to members of the listserv. The School of Behavioral and Brain Sciences at The University of Texas at Dallas is accepting applications at the Ass

[Freesurfer] Freesurfer 5.3 vs 6

Dear Freesurfers Hi I have a bunch of data that is preprocessed in Freesurfer version 5.3 (both recon and preprocessing). My question is whether I can do the first level and group analysis on this data using Freesurfer version 6? Or should I do everything in version 6 from the beginning? I

Re: [Freesurfer] Freesurfer 5.3 vs 6

Hi Mona if you want to compare with another dataset processed with V6, you probably have to reprocess everything in this one with V6 too otherwise you will never know if the differences you are finding are algorithmic or biological. sorry Bruce On Fri, 4 Jan 2019, Nasiriavanaki, Zahra wrote:

Re: [Freesurfer] Freesurfer 5.3 vs 6

Thank you very much Bruce! Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129 From: freesurfer-boun...@nmr.mgh.harvard.ed

[Freesurfer] ROI Analysis

External Email - Use CautionHi everybody,   after finishing my group analysis I am currently trying to run a ROI analysis. However I have some problems/general questions. I am trying to draw a ROI on fsaverage in order to use the mri_label2label command afterwards. I opened Fre

[Freesurfer] gammafit flag in mkanalysis-sess

Hi Freesurfers I have a few questions about gammafit flag in mkanalysis-sess command and I appreciate if you could respond whenever you had time. -How should we decide which function is best to apply on hemodynamic response signal? I have used both spmhrf and gammafit and I see slightly diffe

[Freesurfer] Longitudinal Hippocampal Subfields - error during segmentation

External Email - Use Caution Hello, I have run a longitudinal sample (up to 4 timepoints per subject) through the Freesurfer 6.0 longitudinal processing pipeline, and currently I am attempting to produce the longitudinal hippocampal subfield segmentation with the following com

[Freesurfer] Postdoctoral Fellowship: Neurobiology of Reading {Disarmed}

External Email - Use Caution *Postdoctoral Fellowship: Neurobiology of Reading* The LandiLab (PI: Nicole Landi https://landi.lab.uconn.edu/

Re: [Freesurfer] Freesurfer 5.3 vs 6

but otherwise it is safe to do group analysis with v6 tools on individual data processed with any version of FS On 1/4/19 12:03 PM, Bruce Fischl wrote: Hi Mona if you want to compare with another dataset processed with V6, you probably have to reprocess everything in this one with V6 too otherw

Re: [Freesurfer] gammafit flag in mkanalysis-sess

On 1/4/19 1:27 PM, Nasiriavanaki, Zahra wrote: Hi Freesurfers I have a few questions about gammafit flag in mkanalysis-sess command and I appreciate if you could respond whenever you had time. -How should we decide which function is best to apply on hemodynamic response signal? I have used

Re: [Freesurfer] gammafit flag in mkanalysis-sess

Thank you so much for your helpful reply Doug. MOna Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129 From: freesurfer-boun.

Re: [Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask

External Email - Use Caution Hi Bruce, Thank you, I didn't realize it would be so simple in matlab! To help others who might be looking for a solution: I was able to use MRIread for both my data.mgh file (created using mri_surf2surf, resampled to template space for the thickness v

Re: [Freesurfer] Tracula longitudinal tract reconstruction problems

Hi Nick - This likely means that it got stuck at the initial path for a while, but eventually got unstuck and explored the space successfully. If you don't like this look, you can try setting the nburnin parameter in the config file, to something higher than the default 200. This sets the number

Re: [Freesurfer] Tracula longitudinal tract reconstruction problems

External Email - Use Caution Thank you Anastasia! I’ll try upping the nburnin to 2000, and then I’ve also had some success increasing the nsample to 18000 (which presumably gives it more opportunities to get unstuck and explore?). For the longitudinal pipeline, what’s the best