Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
by Jessica Bourgin 09 Aug '19

09 Aug '19

External Email - Use Caution It seems to work. Thanks a lot ! Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

1 0

CORRECTING DEFECT
by Balken, Brendan 09 Aug '19

09 Aug '19

External Email - Use Caution Hello! So I am attempting to use freesurfer's recon-all script but for one of our subjects I keep getting stuck at this point: "CORRECTING DEFECT 29 (vertices=19321, convex hull=4029, v0=32423) XL defect detected..." It has already corrected 28 defects, but they were much smaller. It has been running for about 48 hours on a very powerful machine and I'm wondering how long I should wait. Will it eventually move on? If no, what is my contingency plan for processing this? I'm using the output anatomy folder in brainstorm for source analysis. Any guidance or information would be greatly appreciated. Thanks a million! Brendan Here's what the lh and rh.inflated.nofix look like (is that the defect?): [cid:image001.png@01D54E9B.E7838030]

2 8

TRACULA - runlist longer than subject list
by Daniel Callow 09 Aug '19

09 Aug '19

External Email - Use Caution Hello, When trying to run TRACULA on my data I keep getting the following error. domainname: Command not found. INFO: SUBJECTS_DIR is /Volumes/DANIEL/freesurfer_Tracy INFO: Diffusion root is /Volumes/DANIEL/dti_Tracy/trac Actual FREESURFER_HOME /Applications/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20190326-01e71dc Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /Applications/freesurfer_dev /Volumes/DANIEL/trac-all -c /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/dmrirc.local -log /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.log -cmd /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.cmd domainname: Command not found. ERROR: run list is longer than subject list I have never had this issue before and have tried multiple options for the run list from () to (1 2 3) to include a number for every subject. However, I always get this error. I wonder if there is some issue with the formatting this go around that could be causing the issue but I can't find it. Below is what I have for the initial part of my dmrirc folder. *# FreeSurfer SUBJECTS_DIR* *# T1 images and FreeSurfer segmentations are expected to be found here* *# * setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_Tracy/ *# Output directory where trac-all results will be saved* *# Default: Same as SUBJECTS_DIR* *#* set dtroot = /Volumes/DANIEL/dti_Tracy/trac *# Subject IDs (one per time point per subject)* *#* set subjlist = (HMN002 HMN003 HMN005 HMN006 HMN007 HMN011 HMN014 HMN018 HMN020 HMN021 HMN022 HMN025 HMN029 HMN035 HMN037 HMN039 HMN045 HMN050 HMN055 HMN057 HMN060 HMN064 HMN065 HMN069 HMN072 HMN073 HMN079 HMN085 HMN087 HMN088 HMN095 HMN097 HMN098 HMN099 HMN101 HMN102 HMN103 HMN105 HMN108 HMN110 HMN112 HMN113 HMN115 HMN118 HMN120 HMN121 HMN123 HMN135 HMN141 HMN144 HMN152 HMN156 HMN160 HMN163 HMN175 HMN180 HMN186 HMN187 HMN189 HMN190 HMN191 HMN193 HMN195 HMN196 HMN200 HMN201) *# Longitudinal base template subject IDs (one for each time point above)* *#* set baselist = () *# In case you want to analyze only Huey and Louie* *# Default: Run analysis on all time points and subjects* *#1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66* set runlist = () *# Input diffusion DICOMs (file names relative to dcmroot)* *# If original DICOMs don't exist, these can be in other image format* *# but then the gradient table and b-value table must be specified (see below)* *#* set dcmroot = /Volumes/DANIEL/Tracy/HMN_W1 set dcmlist = ( HMN002/image000001.dcm HMN003/image000001.dcm HMN005/image000001.dcm HMN006/image000001.dcm HMN007/image000001.dcm HMN011/image000001.dcm HMN014/image000001.dcm HMN018/image000001.dcm HMN020/image000001.dcm HMN021/image000001.dcm HMN022/image000001.dcm HMN025/image000001.dcm HMN029/image000001.dcm HMN035/image000001.dcm HMN037/image000001.dcm HMN039/image000001.dcm HMN045/image000001.dcm HMN050/image000001.dcm HMN055/image000001.dcm HMN057/image000001.dcm HMN060/image000001.dcm HMN064/image000001.dcm HMN065/image000001.dcm HMN069/image000001.dcm HMN072/image000001.dcm HMN073/image000001.dcm HMN079/image000001.dcm HMN085/image000001.dcm HMN087/image000001.dcm HMN088/image000001.dcm HMN095/image000001.dcm HMN097/image000001.dcm HMN098/image000001.dcm HMN099/image000001.dcm HMN101/image000001.dcm HMN102/image000001.dcm HMN103/image000001.dcm HMN105/image000001.dcm HMN108/image000001.dcm HMN110/image000001.dcm HMN112/image000001.dcm HMN113/image000001.dcm HMN115/image000001.dcm HMN118/image000001.dcm HMN120/image000001.dcm HMN121/image000001.dcm HMN123/image000001.dcm HMN135/image000001.dcm HMN141/image000001.dcm HMN144/image000001.dcm HMN152/image000001.dcm HMN156/image000001.dcm HMN160/image000001.dcm HMN163/image000001.dcm HMN175/image000001.dcm HMN180/image000001.dcm HMN186/image000001.dcm HMN187/image000001.dcm HMN189/image000001.dcm HMN190/image000001.dcm HMN191/image000001.dcm HMN193/image000001.dcm HMN195/image000001.dcm HMN196/image000001.dcm HMN200/image000001.dcm HMN201/image000001.dc) Any help debugging the issue would be greatly appreciated! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

2 2

TRACULA - OrientLAS issue for a subject
by Daniel Callow 09 Aug '19

09 Aug '19

External Email - Use Caution Hello, I am running TRACULA on my data set and am having issues with one of my subjects. For this subject, I get the following error. INFO: input image orientation is LIS INFO: input image determinant is 18.4229 rdc_new: Undefined variable. rdc_new: Undefined variable. rdc_new: Undefined variable. ny_new: Undefined variable. I have attached the dcminfo.dat file of this subject. It seems like mri_info is having trouble either extracting or writing cdc, rdc, and sdc values from this subject's dcminfo.dat file? Any idea why this might be? I have looked through this subjects dcminfo.dat file and compared it to others but have been unable to identify the issue. I have also included the trac-all log for this subject. Some advice on what the issue might be would be greatly appreciated! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

1 0

Hippocampal subfields
by 郑凤莲 09 Aug '19

09 Aug '19

External Email - Use Caution Hi exports, I am using FS6.0 to segment hippocampus. I run "recon-all -s bert -hippocampal-subfields-T1" and it said "recon all bert finished without error". However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And in tmp directory, there are two directories, "hippoSF_T1_v10_left" and "hippoSF_T1_v10_right". But in these two directories, the l(r)h.hippoSfLabels-T1.v10.mgz file is still not exsit. What's the matter? I need your help. Thanks very muxh in advance. Sincerely, Zheng

2 3

Avoiding or removing overlap when converting surface labels to volume
by Jacob Miller 08 Aug '19

08 Aug '19

External Email - Use Caution Hi Freesurfer team, I am transforming several adjacent surface labels into volume ROIs, using *mri_label2vol*. When doing so, there seems to be some possibly unavoidable overlap in a small number of voxels in the volume ROIs. Is there any way to avoid these labels from overlapping when transformed into the volume? I see that *mri_label2vol* takes an --annot flag, would this help in avoiding overlap in the outputs? Otherwise, I can remove the overlapping voxels int he nifti file outputs, but I was wondering if the algorithm had any options to do this as part of the surface-to-volume transform. Thanks so much! Jacob -- Jacob Miller Graduate Student, D'Esposito Lab Helen Wills Neuroscience Institute (HWNI) University of California, Berkeley https://despolab.berkeley.edu/

1 0

TRACULA empty bbr maps after trac-all -prep
by Fred Sampedro 08 Aug '19

08 Aug '19

External Email - Use Caution Dear TRACULA experts, dear Anastasia, I've been successfully using TRACULA for a while with different DTI images from different scanners (siemens, philips...). Now I am working with GE DTI data and whereas the trac-all -prep command went well, and $subject/dmri/dtifit_FA.nii.gz and dtifit_MD.nii.gz look fine, $subject/dmri/mni/dtifit_FA.bbr.nii.gz and all mni-space maps are empty (see pictures attached). I also attach the trac-all.log file. and bvals/bvecs that were generated by trac-all directly from the dicom images. What could have gone wrong?

2 1

Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
by Iglesias Gonzalez, Juan E. 08 Aug '19

08 Aug '19

Please try using the 1mm version of the segmentation in FreeSurfer space. Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Jessica Bourgin <jessica.bourgin(a)univ-smb.fr> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, 8 August 2019 at 11:58 To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space External Email - Use Caution Dear Juan Eugenio, Thank you for these precisions. Following the guidelines of FSL, I computed the following sequence on my structural image : bet my_structural my_betted_structural flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_structural --warp=my_nonlinear_transf --out=my_warped_structural The warped structural image overlapped nicely with the atlas. However, when I compute the following command on the segmentations : applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=freesurfer/lh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf --out=my_warped_lh applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=freesurfer/rh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf --out=my_warped_rh The segmentations do not appear on the atlas nor the structural image. Do you know how to solve this problem ? Thanks for your help. PS: I used FSL for registration because I don't know how to do that with Freesurfer. Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

1 0

Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
by Jessica Bourgin 08 Aug '19

08 Aug '19

External Email - Use Caution Dear Juan Eugenio, Thank you for these precisions. Following the guidelines of FSL, I computed the following sequence on my structural image : bet my_structural my_betted_structural flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_structural --warp=my_nonlinear_transf --out=my_warped_structural The warped structural image overlapped nicely with the atlas. However, when I compute the following command on the segmentations : applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=freesurfer/lh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf --out=my_warped_lh applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=freesurfer/rh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf --out=my_warped_rh The segmentations do not appear on the atlas nor the structural image. Do you know how to solve this problem ? Thanks for your help. PS: I used FSL for registration because I don't know how to do that with Freesurfer. Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

1 0

SegmentHA_T1.sh hippocampal sub-field issue
by Daniel Callow 08 Aug '19

08 Aug '19

External Email - Use Caution Hello, When using segmentHA_T1.sh on one of my subjects the left hippocampus ROI seems to spill over a lot into white matter and other gray matter regions. See attached picture. Is there a way to fix this or improve the hippocampal segmentation? Or will I have to scrap this subject's data? I have also included the scan log. Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer