[Freesurfer] TRACULA - OrientLAS issue for a subject

2019-08-15 Thread Daniel Callow
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

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

2019-08-15 Thread Mahshid Fouladivanda
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

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

2019-08-15 Thread Dylan Nielson
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

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

2019-08-15 Thread Collins Jones, Liam
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

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

2019-08-15 Thread Tim Schäfer
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,

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

2019-08-15 Thread Bruce Fischl
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] Using Freesurfer Commands for Neonate

2019-08-15 Thread Mahshid Fouladivanda
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

Re: [Freesurfer] apart.a2009s naming convention: from "_and_" to "&"

2019-08-15 Thread Tim Schäfer
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

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

2019-08-15 Thread Mahshid Fouladivanda
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"

Re: [Freesurfer] apart.a2009s naming convention: from "_and_" to "&"

2019-08-15 Thread Tim Schäfer
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

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

2019-08-15 Thread Tim Schäfer
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

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

2019-08-15 Thread Reza Rahmanzadeh
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

Re: [Freesurfer] mri_vol2vol

2019-08-15 Thread Greve, Douglas N.,Ph.D.
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

Re: [Freesurfer] spatial scale bar question

2019-08-15 Thread Nasiriavanaki, Zahra
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

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

2019-08-15 Thread Jamie Hanson
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 (

[Freesurfer] Conversions between MNI152, MNI305 & surface

2019-08-15 Thread Lauri Tuominen
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

[Freesurfer] mri_vol2vol

2019-08-15 Thread Rihana Rayan
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