[Freesurfer] Differences between version 5.2.0 and 6.0.0

I want to ask about differences in brain segmentation with freesurfer version 5.2.0 and 6.0.0. My dicom data have original size 0.375x0.375x0.75 mm and 600, 640, 224 voxels. If I process the data vith the version 5.2.0, freesurfer conformed the data to 1 mm size and 256 voxels for all directions.

[Freesurfer] dev version

Hi all experts, I am using freesurfer dev version for segmentation of hippocampus and amydala. I have a doubt about it. 1. In FS 6.0, I can type '203-226' in freeview for viewing subfields of hippocampus. In dev version, When I type 'freeview -v nu.mgz -v lh.hippoAmygLabels-T1.v2x.FS60.mgz:c

[Freesurfer] Fw: Postdoc fellowship at Merck

A two-year postdoctoral fellowship in the Center for Observational and Real-World Evidence (CORE) division at Merck, applying quantitative methods to improve healthcare quality/outcomes and reduce cost: https://taleo.msd.com/careersection/merck_external_career_section/jobdetail.ftl?job=POS00024

[Freesurfer] Spatial smoothing during preprocessing

Hi all, I read from the freesurfer discussion archives that when combining FSL FEAT with freesurfer, one should definitely NOT do spatial smoothing in the preprocessing when preparing to examine cortical data. https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11536.html However I ca

[Freesurfer] segmentHA_T2.sh

Dear freesurfer experts, I have tried the dev version of Segmentation of hippocampal subfields and nuclei of the amygdala for OSX el Capitan, downloaded today. I did get an error message similar to a previous error I found on this mailing list: https://mail.nmr.mgh.harvard.edu/pipermail//freesurf

[Freesurfer] How to extract stats of the regions that is covered by large clusters

Hello Experts: After running mri_glmfit sim, I got below clusters: ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow CWPHi NVtxsWghtVtx Annot 1 16.567 56197 13752.71-36.8 -15.5 55.0 0.00020 0.0 0.00040 30900 180209.80 precentral

[Freesurfer] mri_aparc2aseg labelwm not labelling wm

Freesurfers, I am trying to use a cortical label to label wm. I am using the following command line: mri_aparc2aseg --s $patient --annot 8V1 –labelwm And most of the time in most subjects this works, however sometimes the output file doesn’t label any wm with the 3000+N or 4000+N like it usuall

Re: [Freesurfer] Yendiki Anastasia config file

Hi – There are a few places in the config file where the variable “$TUTORIAL_DATA” is referenced. Do you define that variable on your own before your run trac-all? If not, you have to edit the config file and replace it everywhere with the path to where you saved the tutorial data on your comput

[Freesurfer] Yendiki Anastasia config file

Here is the configuration file. I think is the default by tutorial. dmrirc.tutorial Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in th

Re: [Freesurfer] [External] Re: Issue with mri_convert on centOS 7

Hi Danielle if you send me the two input volumes (don't cc the list) I'll see if we can replicate and fix this problem. cheers Bruce On Wed, 31 Jan 2018, Cooke,Danielle ( BIDMC - Neurology ) wrote: Hi Bruce, This is the command and output on a CentOS 7 machine: [dc155@pinto DANI]$ mri_con

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Hello Dr. Greve, Yes it exists. The output below was with debug option. Best Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, January 30, 201

Re: [Freesurfer] [External] Re: Issue with mri_convert on centOS 7

Hi Bruce, This is the command and output on a CentOS 7 machine: [dc155@pinto DANI]$ mri_convert 3062.nii.gz -rl MNI152_T1_2mm_brain.nii.gz 3062_MNI.nii.gz mri_convert 3062.nii.gz -rl MNI152_T1_2mm_brain.nii.gz 3062_MNI.nii.gz $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ readin

[Freesurfer] Longitudinal TRACULA study

Hi, I want to clarify some aspects longitudinal TRACULA processing before processing my data. For example, I have 3 timepoints of data of the same participant: sub101_01 sub101_02 sub101_03 All of these have structural and diffusion data (same scanner, same acquisition parameters). I processe