Re: [Freesurfer] Skullstriping problems

Hi Mateus, Please attach the recon-all.log file for your subject and I will take a look. Best, Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of MATEUS ROZALEM ARANHA Sent:

Re: [Freesurfer] recon-all on newborn

Hi Sarbani, Please see this paper for more information: https://www.ncbi.nlm.nih.gov/pubmed/25741260 Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Das S. Sent: Friday, July 7,

Re: [Freesurfer] Skullstriping problems

anks, Emma From: MATEUS ROZALEM ARANHA <mateus.ara...@hc.fm.usp.br> Sent: Thursday, August 17, 2017 6:18:28 AM To: Freesurfer support list; Boyd, Emma Subject: Re: [Freesurfer] Skullstriping problems Hi Emma, Could you take a look at the recon-all.log file I sent you? Best Ma

Re: [Freesurfer] Mris_volume

Thank you! On Wed, Sep 20, 2017 at 5:15 PM Boyd, Emma <ebo...@mgh.harvard.edu<mailto:ebo...@mgh.harvard.edu>> wrote: Hi Fereshte, mris_volume does not create any output files, that number you see in the terminal is the total volume of a given closed surface. Try running mris_v

Re: [Freesurfer] Mris_volume

Hi Fereshte, mris_volume does not create any output files, that number you see in the terminal is the total volume of a given closed surface. Try running mris_volume -v instead and you will see something like this in your terminal: reading ... surface file read in. Volume computation took

Re: [Freesurfer] Extracting labels using mri_watershed

behalf of Fereshte <fereshte.ramez...@gmail.com> Sent: Sunday, October 15, 2017 6:43:08 AM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting labels using mri_watershed Hi Emma, I've tried this before but surprisingly not such labels in the output volume. On Wed, Oct 11, 2017 at

Re: [Freesurfer] Freesurfer tutorial

Hi Eva, Have you taken a look at the help text for mri_segstats (mri_segstats --help)? The information under 'summary file format' and 'examples' may be helpful. Also, this page might have some helpful information for you on working with FreeSurfer stats files:

Re: [Freesurfer] Recon-all error

Hi Bronwyn, Doug is out of the office today. What is the command you ran after deleting everything in the surf folder? Can you send us the recon-all.log? Best, Emma - Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical

Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

derson <john.ande...@protonmail.com> Sent: Thursday, August 31, 2017 3:25:43 PM To: Boyd, Emma Cc: Freesurfer support list Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz Hi Emma, Thank you for your response. I am running my recons using V5.3 and V6.0 In the data base I have ~200 T1 images and for

Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

Hi John, Which version of FreeSurfer are you running? Emma - Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Extracting labels using mri_watershed

Hi Fereshte, mri_watershed -LABEL inputvolume.mgz outputvolume.mgz The output volume will contain 6 labels: 0 = exterior 1 = scalp 2 = skull 3 = csf 4 = gray 5 = white 6 = fat tissue Emma > On Oct 11, 2017, at 3:38 AM, Fereshte wrote: > > Dear Experts, > How is

Re: [Freesurfer] Erroneous output after recon-all: Bad segmentation and surfaces

Hi Arsenije, If you've already tested out different watershed thresholds and gcut, then yes, the next step would be to manually erase these voxels and reprocess. The ventricle labeling is a separate problem - which version of FreeSurfer are you running? Best, Emma - Emma Boyd

Re: [Freesurfer] non-brain region

Hi Ramesh, Unless these non-brain regions affect the surfaces then it is fine to leave it as is. Your image looks fine to me. Emma - Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging

Re: [Freesurfer] Infant Atlas

Hi Lemon Please see the mailing list archive here for some guidance (the answer is the same for infants): https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56037.html I couldn't see the UNC link you provided. But the basic steps for creating your own atlas are: -label every

Re: [Freesurfer] Extracting labels using mri_watershed

t; and the output file is attached. Thank you in advance Fereshte On Mon, Oct 16, 2017 at 6:45 PM Boyd, Emma <ebo...@mgh.harvard.edu<mailto:ebo...@mgh.harvard.edu>> wrote: Interesting.. would you mind sending me the command you ran and file drop the input and output volumes to me?: https://

Re: [Freesurfer] aparcstat2table with new destrieux atlas

Hi Lisa, Have you tried using the --parc flag to specify the parcellation atlas you want? Run aparcstats2table --help for more information. Best Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lisa

Re: [Freesurfer] mpr2mni305 talaraich transformation error

Hi Aicha, Have you visually inspected your input image, rawavg.mgz or orig.mgz to make sure they look ok? Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Dijkshoorn, A.B.C. (Aicha)

Re: [Freesurfer] Control Points Not Working

Hi Arsenije, You should never need to add hundreds of control points, just a few dispersed through the problematic area should work. Would you mind uploading your recon to our file drop site and I'll take a look at it? You can send it to my email, ebo...@nmr.mgh.harvard.edu.

Re: [Freesurfer] GC-DG

Hi Zheng, GC-DG stands for granule cell layer of the dentate gyrus. For more information on how this area was manually segmented, please see Eugenio’s paper here: http://www.nmr.mgh.harvard.edu/~iglesias/pdf/subfieldsNeuroimage2015preprint.pdf Emma Emma Boyd Research Technician II Laboratory

Re: [Freesurfer] Errors preprocess

Hi Seonjoo, What directory are you in when you run preproc-sess? You should run this command from the data/ dir. Emma - Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging From:

Re: [Freesurfer] FreeSurfer Error Edit Sequence

Hi David, Please see my response here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57251.html Best Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of David S Lee

Re: [Freesurfer] FreeSurfer Edit Sequence Inquiry

Hi David, There is no particular order in which you have to make edits. The order in which these edits are described on our wiki is not indicative of any order in which they must be made. However, it may help you to understand the overall order of the recon-all processing stream so that you

Re: [Freesurfer] DICOM input to recon-all

Hi Karin, This tutorial will explain how to find your dicom input file: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice Best, Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Karin Westin

Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047

Hi Jeongson, I took a look at your data, thank you for uploading it. Your recon is likely failing because your case has a large pathology that is causing your white matter surface to be topologically incorrect. I recommend filling in that whole area on the wm.mgz mask and re-running the rest