Re: [Freesurfer] AAL and freesurfer atlas concordance

External Email - Use Caution Dear All I have seen posts discussing about bringing AAL to freesurfer etc. I am wondering whether anyone has created a table of concordance between the regions in AAL to the freesurfer or the vice versa. If so can you please share with me. For my wo

Re: [Freesurfer] Flipped left to right hemisphere subjects

Is the volume actually left-right reversed? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lutz,Olivia (BIDMC - Psychiatry) Sent: Monday, August 20, 2018 4:55:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Flipped left to right h

[Freesurfer] Fw: Parcellation label error

External Email - Use Caution From: Ali,Mohamed Tarek Mohamed Sent: Saturday, August 18, 2018 10:59 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Parcellation label error Hello FreeSurfer Developers, While I am using [vec,labels,cnames] = read

Re: [Freesurfer] Flipped left to right hemisphere subjects

Hi Doug and Bruce, thank you for the quick reply. As a follow-up question, we've edited our brainmasks for a dataset and want to flip some subjects left to right. I found instructions to flip the scans, however they are for the nu.mgz file (https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightRe

[Freesurfer] correlation between blood biomarkers and longitudinal decrease in cortical thickness

External Email - Use Caution Hello, I have done freesurfer (v6) longitudinal preprocessing for 20 subjects (baseline and 2-year follow-up). We also have levels of some blood biomarkers (e.g. tau, neurofilament light) for these subjects at the baseline. I am interested to figure

Re: [Freesurfer] segmentHA_T1.sh exits with error

External Email - Use Caution Dear Antonin, Thanks again for letting us know you had this problem; it turned out to be a small, silly bug in the code. I will fix it ASAP, and the updated code should be on the dev version in the next few days. Cheers, /Eugenio -- Juan Eugenio Igle

[Freesurfer] How to register fMRI data without upsampling voxel size?

External Email - Use Caution Dear Freesurfer experts, Could you please let me know how to normalize fMRI data without upsampling the original voxel size from 5 x 5 x 7 mm to 2 x 2 x 2 mm? I have tried this as follows: 1. Register functional (data.nii) to anatomical matrix

[Freesurfer] How to install Biomedical Toolkit examples in Labview 2015?

External Email - Use Caution Hi freesurfers, Does anyone know how to install Biomedical Toolkit examples in Labview 2015? I installed an evaluation version of Labview 2015, 2015DFDT, and 2015ASPT under Windows 7. Then, I installed the 2014BMTK but only one, I get the Biomedical

Re: [Freesurfer] Lesion segmentation

External Email - Use Caution Hi everyone, I apologize for reposting this but I haven't received any response since last week. Could someone pls help? Here are my questions: 1) What is considered a lesion in subcortical segmentation? (tumor, MS, stroke, etc) 2) Would you pls sha

[Freesurfer] 3 positions to post

External Email - Use Caution Hi, I want to post a positions bellow, thanks to reply where I should go to post it on free surfer please. Best, Florence Postdoctoral Position on Imaging Genetics.docx Description: MS-Word 2007 document Research Engineer.docx Description: MS-Word

Re: [Freesurfer] Freesurfer v6.0: Using FLAIR for hippocampal subfields

External Email - Use Caution Without having seen your FLAIR scans, I’d say probably not, but it’s an empirical question; give them a go! ;-) -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesi

[Freesurfer] Freesurfer v6.0: Using FLAIR for hippocampal subfields

External Email - Use Caution Dear freesurfer experts, I'm interested in doing subfield segmentations of the hippocampus in version 6.0. What I am specifically interested in, is that if I can expect better segmentations if I use a 1mm isotropic FLAIR series in addition to the 1mm i

[Freesurfer] AAL and freesurfer atlas concordance

External Email - Use Caution Dear All I have seen posts discussing about bringing AAL to freesurfer etc. I am wondering whether anyone has created a table of concordance between the regions in AAL to the freesurfer or the vice versa. If so can you please share with me. For my wor