Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

How to run part of TRACULA
by Athanasia Metoki 15 Aug '16

15 Aug '16

Dear Freesurfer Developers, I am fairly new to image analysis and this is the first time I use Freesurfer. I have some DTI data and I have already preprocessed them and ran bedpostX using FSL. I ran probabilistic tractography on FSL as well to get the connectivity between two distinct brain areas. I am also interested in getting the probability distribution for the uncinate fasciculi so I am trying to use TRACULA. My question is: Can I use TRCULA without doing preprocessing and dedpostX again? If so, will I need to do the cortical parcelation and subcortical segmentation with recon-all and get the aparc+aseg.mgz file in order to use TRACULA? Which argument would I need to use when I run recon-all? Thank you! *Athanasia Metoki* Psychology Doctoral Student - Brain and Cognitive Sciences Program Cognitive Neuroscience Laboratory Temple University Department of Psychology 1701 N 13th St. Philadelphia, PA 19122 Email: athanasia.metoki(a)temple.edu _______________________________________________________________________________ The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited.

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TRACULA extracting diffusion measures using ASEG or WM parc
by Chung, Yoonho 15 Aug '16

15 Aug '16

Hi Anastasia, Is it possible to extract diffusion measures FA, ADC etc. within the subcortical (ASEG) or WM parc ROI regions using the Freesurfer tools? If possible, can you show how it can be done? Thank you in advance. Best, Yoon

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Fwd: Recon-all with flair
by Eelco van Duinkerken 15 Aug '16

15 Aug '16

Dear FreeSurfers, I've been preprocessing, in FS5.3, 3T GE data in controls, obese and diabetes patients and adding the available flair to do the pial refinement as follows: recon-all -i t1 -s bla -all -FLAIR flair -FLAIRpial This works excellent for most of the scans. Unfortunately, for some scans adding the flair leads to some interesting refinements, either extending outside of the brain.mgz or going deep into the white matter. I didn't notice any misregistrations of the flair to the T1 scan when checking the bb-registration, nor were there any errors in the recon-all.log. I have added some screenshots. The red lines represent the pial with the flair refinement, and the blue lines the pial without the refinement. As you can see, these interesting segmentations are not there when the flair is no used. Does anyone know what is going on? Thanks a lot, Eelco

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Fwd: mri_preproc error
by YoungHoon Kwon 15 Aug '16

15 Aug '16

---------- Forwarded message ---------- From: YoungHoon Kwon <yhkn11(a)gmail.com> Date: 2016-07-13 21:10 GMT-04:00 Subject: mri_preproc error To: freesurfer(a)nmr.mgh.harvard.edu Hello FreeSurfer Developers, I tried to assemble the data by using mri_preproc, then it shows segmentation fault (core dumped) after running. I searched for the solution, but I couldn't find it. Here's information Error : Segmentation fault (core dumped) Input : FS.txt (FSGD file) GroupDescriptorFile 1 Title All Class Male Class Female Input 002_S_4213_A Male Input 002_S_4225_A Male Input 002_S_4262_A Female command: [knho@in-rady-neuro11 test]$ mris_preproc --fsgd FS.txt \ --target fsaverage --hemi lh \ --meas thickness \ --out practice_result.mgh nsubjects = 3 tmpdir is ./tmp.mris_preproc.2677 /localscratch3/test Log file is practice_result.mris_preproc.log Wed Jul 13 19:31:44 EDT 2016 setenv SUBJECTS_DIR /localscratch3/test cd /localscratch3/test /net/age3/DATA_from_AGE0/FREESURFER/freesurfer51/bin/mris_preproc --fsgd FS.txt --target fsaverage --hemi lh --meas thickness --out practice_result.mgh Linux in-rady-neuro11.indyrad.iupui.edu 3.16.2-201.fc20.x86_64 #1 SMP Mon Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.2677 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/3 002_S_4213_A Wed Jul 13 19:31:44 EDT 2016 -------------- ----------------------- mri_surf2surf --srcsubject 002_S_4213_A --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.2677/002_S_4213_A.1.mgh --sval /localscratch3/test/002_S_4213_A/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped) I found some advice from online, and it suggested to run recon-all; however it didn't work. I really don't know what is wrong. Can anyone figure out this error? 1) Versioin : FreeSurfer 5.1 2) Platform : Linux 3) uname -a : Linux in-rady-neuro11.indyrad.iupui.edu 3.16.2-201.fc20.x86_64 #1 SMP Mon Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

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FreeSurfer TrackVis Transforms
by "김재명" 15 Aug '16

15 Aug '16

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TRACULA tract endpoints on cortical surface
by Barbara Kreilkamp 13 Aug '16

13 Aug '16

Dear Freesurfers and TRACULA experts, Thank you for your help so far. I am trying to map the endpoints of the tract probability distributions onto the cortical surface (as mentioned in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos). I've somehow gathered that I need to do this (example one endpoint): flirt -ref /mri/orig/T1.nii.gz -in dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init /dmri/xfms/diff2anat.bbr.mat I then loaded the images in Freeview and they look reasonable together with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz What I don't get is how to do this: "we projected the tract endpoints onto the gray/white matter surface by sampling along the surface normal vector, anywhere within 6 mm (3 DWI-space voxels) of the gray/white junction and then smoothing along the surface with a 2D Gaussian kernel of 6mm full width at half max." (Solsnes et al. 2016) Any help would be greatly appreciated. Best wishes, Barbara

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repost aseg.mgz error
by Jasmin Alves 12 Aug '16

12 Aug '16

Dear Freesurfer I encountered an error on the aseg mask for a participant, both hemispheres for the aseg appear on one hemisphere of the brain mask. I ran it a few times and I also used different T1s but it consistently showed this error. Is there a way I can correct this? Thanks, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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FW: TRACULA re-init error
by Song, Daniel 12 Aug '16

12 Aug '16

Dan ________________________________ From: Ostrowski, Lauren Sent: Monday, August 08, 2016 4:08 PM To: Song, Daniel Subject: FW: TRACULA re-init error ________________________________ From: Ostrowski, Lauren Sent: Monday, August 08, 2016 4:04 PM To: Freesurfer(a)nmr.mgh.harvard.edu Subject: TRACULA re-init error Hi all, I'm running into a problem with TRACULA, when I try to re-initialize tracts that failed to reconstruct during the first run. I have set reinit = 1 in the configuration file and specified the particular tracts that I want to reconstruct, but when I try to run the "trac-all -prior" step, I keep getting this error message: INFO: SUBJECTS_DIR is /autofs/cluster/neuromind/cat/bects/subjects INFO: Diffusion root is /cluster/neuromind/cat/bects/subjects/pBECTS001/trac Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/dev trac-preproc -c /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/dmrirc.local -log /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/trac-all.log -cmd /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/dev/bin/trac-preproc #------------------------------------- #@# Priors Mon Aug 8 15:53:46 EDT 2016 /usr/local/freesurfer/dev/bin/dmri_train --outdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni --out fmajor_PP_avg33_mni_bbr --slist /tmp/subj33.pBECTS001.15581.txt --trk dlabel/mni/fmajor_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 --rois dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz --bmask /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz --cptdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff --reg /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc ERROR: fio_pushd: /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni cwd /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/dlabel/mni cmdline /usr/local/freesurfer/dev/bin/dmri_train --outdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni --out fmajor_PP_avg33_mni_bbr --slist /tmp/subj33.pBECTS001.15581.txt --trk dlabel/mni/fmajor_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 --rois dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz --bmask /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz --cptdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff --reg /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc sysname Linux hostname truffles machine x86_64 user lo941 Output directory: /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni Output directory in test subject's space: /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff Output base: fmajor_PP_avg33_mni_bbr Training subject directory list: /tmp/subj33.pBECTS001.15581.txt Location of streamline files relative to base: dlabel/mni/fmajor_PP.bbr.trk Location of start ROI files relative to base: dlabel/mni/fmajor_PP_roi1.bbr.nii.gz Location of end ROI files relative to base: dlabel/mni/fmajor_PP_roi2.bbr.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux truffles 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Aug 8 15:53:46 EDT 2016 Any help would be very much appreciated. It seems to me that TRACULA can't find the aparc+aseg labels, but when I looked at the aparc+aseg nifty file, the parcellations and labels all seem correct. Thanks, Lauren Ostrowski

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Recon-all
by Heidi Foo 12 Aug '16

12 Aug '16

Hi FreeSurfer Team, I have done recon-all using FS 5.3 and I would like to run the recon-ed images from 5.3 in FS 6.0. May I know how I should go about doing that? Thank you. Regards, Heidi Foo

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Postdoctoral Position in pediatric imaging: Boston Children's Hospital/Harvard Medical School
by Gaab, Nadine 12 Aug '16

12 Aug '16

Postdoctoral Position at Boston/Children's Hospital & Harvard Medical School The GaabLab (gaablab.com)<gaablab.com> at the Laboratories of Cognitive Neuroscience in collaboration with the Fetal-Neonatal Neuroimaging and Developmental Science Center<https://urldefense.proofpoint.com/v2/url?u=https-3A__fnndsc.babymri.org_&d=…> at Boston Children's Hospital invites applications for a NICHD funded post-doctoral associate in the area of developmental cognitive neuroscience/pediatric (f)MRI. Available resources include a 3.0T MRI scanner, a child-friendly Mock scanner and analysis platforms based in MATLAB/UNIX. The candidate will be expected to oversee the analysis of pediatric and infant (f)MRI experiments, analyze behavioral and (f)MRI data, develop new analysis tools, prepare manuscripts for publication, and participate in conferences. The NICHD funded project aims to characterize trajectories of early structural, functional, and metabolic brain development in infants with and without a familial risk of developmental dyslexia, and intergenerational transmission of brain alterations associated with language-based learning disabilities will further be examined. The successful applicant should have a doctoral degree in a field related to developmental cognitive neuroscience (e.g., cognitive neuroscience, neuroscience, psychology, developmental psychology, medicine) or a background in electrical engineering, biomedical engineering or computer science. The successful applicant must possess excellent English verbal and written communication skills. Applicants are expected to have a very strong research background in the design and analysis of functional brain-imaging experiments. Experience with (f)MRI analyses programs (e.g., SPM, FSL, Freesurfer, AFNI) a must. Programming skills (MATLAB, C++; Python) are desirable and experience with MVPA or connectivity analyses a plus. Experience with the analysis of pediatric neuroimaging data sets and language and reading research are useful. Approximate start date is fall 2016 (the earlier the better). Successful applicants will be appointed at Children's Hospital Boston and Harvard Medical School. For consideration please send a statement of interest, a CV and a list of three potential referees via email to Nadine Gaab, PhD (nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu>). The search will continue until the position is filled. "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955) Nadine Gaab, PhD Associate Professor of Pediatrics Boston Children's Hospital/Harvard Medical School Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience Mail stop code: BCH3178 1 Autumn Street (Office 643); Boston, MA 02115 nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu> phone: 857-218-3021 www.gaablab.com<http://www.gaablab.com>

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