Re: [Freesurfer] mri_vol2vol

You shoul use mri_label2vol with ROI.nii as the --seg input. How do you know that --regheader is right? On 8/15/19 3:13 PM, Rihana Rayan wrote: > > External Email - Use Caution > > Dear FS users, > I have performed recon-all on structural data and created ROIs (using > mri_binarize), I w

[Freesurfer] Conversions between MNI152, MNI305 & surface

External Email - Use Caution Hello! I keep having 2 somewhat related problems: 1. How to convert a single coordinate from MNI305 to surface. Previosly Doug suggested to try the example 8b in https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems. However, that one is about

Re: [Freesurfer] spatial scale bar question

Hi Freesurfer experts I wanted to follow up on my question about "spatial scale bar" for significancy maps in FS. I appreciate if you let me know about the updates on that. Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massach

[Freesurfer] Question re: hippocampal & amygdala subdivision files.

External Email - Use Caution Dear Freesurfer List, I had a (hopefully) quick question re: output files from the hippocampal and amygdala subdivision routines. I know that there are multiple parcel schemes for the hippocampus (HBT, FS60, and CA), and per this thread ( https://www.m

[Freesurfer] mri_vol2vol

External Email - Use Caution Dear FS users, I have performed recon-all on structural data and created ROIs (using mri_binarize), I want to mask functional data (GLM beta) with ROIs. To match the file sizes, I resampled the ROI.nii by performing the command: mri_vol2vol --mov ROI.ni

Re: [Freesurfer] mris_convert segmentation fault on R hemisphere aparc.a2009s only?

Hi Damion if you upload the relevant files so that we can replicate this we will fix it cheers Bruce On Wed, 14 Aug 2019, Damion V Demeter wrote: External Email - Use Caution I am having an issue processing some of my subjects through the HCP pipeline and have no idea what

Re: [Freesurfer] mri_robust_template in FMRIprep rotation should not scale error

External Email - Use Caution Thanks for taking a look at this Martin. I've uploaded the files to my google drive, you should be able to find them here: https://drive.google.com/open?id=1GmdgXr0kFP10YYw6Wk8Vio7_dcZHNYL4 I've put each subject in their own directory along with the in

[Freesurfer] TRACULA - OrientLAS issue for a subject

External Email - Use Caution For reference, I think the issue had to do with the orientation of these two subjects. I added tome code to use 3dwarp -deoblique to the dwi_orig.nii.gz and then ran orientLAS and it worked this time. The only thing I am unsure about is if this will nu

Re: [Freesurfer] Issues with set-up and configuration on Linux

External Email - Use Caution There is a misconfiguration in your system. It seems that various important Linux directories (like /bin/) are not in your PATH environment variable, and thus your shell is not functional anymore because required standard software (tr, sed, grep, cp,

[Freesurfer] Issues with set-up and configuration on Linux

External Email - Use Caution Dear FreeSurfer developers, I am having trouble with FreeSurfer set up and configuration on Linux. The installation appears to have completed without any problems, though when pasting the lines export FREESURFER_HOME=/usr/local/freesurfer source $FR

Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help

External Email - Use Caution Dear Doug, I have to come back to you for helps as yet i did not find a solution for Group analysis of inflated cortex for NDI and ODI maps of NODDI. What i know is: 1- when i load the output of mris_preproc (regardless of using the old and new ve

Re: [Freesurfer] Using Freesurfer Commands for Neonate

External Email - Use Caution Dear Lilla, Thanks for your help. I have used the same command in the recon-all.log file (seen bellow), but I have a doubt for the highlighted part in the command: "mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mg

Re: [Freesurfer] How to Divide the Brain Surface Parcells to more regions

External Email - Use Caution Dear Doug, Special appreciation for your help. Actually, I have created the annotation and the color table files and finally I have divided the parcels. Also, I checked the primary and the division parcels on the .pial surface that they were corr

Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?

External Email - Use Caution Dear Doug, Here is the emails: Message: 6 Date: Fri, 2 Aug 2019 01:55:34 + From: "Greve, Douglas N.,Ph.D." Subject: Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"? To: "freesurfer@nmr.mgh.harvard.edu" Message-ID

[Freesurfer] FreeSurfer 6 vertex-wise cortical volume computation details?

External Email - Use Caution Dear FreeSurfer experts, can anybody refer me to a publication that explains in detail how vertex-wise cortical volume (the data in /surf/?h.volume) is computed in FreeSurfer 6? My understanding is the following: * area is computed as 1/3 the area

freesurfer@nmr.mgh.harvard.edu

External Email - Use Caution Another interesting thing I noticed, which may be of interest to anybody parsing label data: in the ABIDE data (5.x), labels without any assigned vertices are not listed at all for subjects. So if you want to find all label names of an atlas, you can

freesurfer@nmr.mgh.harvard.edu

External Email - Use Caution Yes, this has indeed also caused me some confusion. I took the label names from fsaverage (and thus from my v6 installation), parsed ABIDE structural data (5.x) and wondered why there was no data in there for most atlas labels. I was quite sure it wa