Freesurfer August 2016

freesurfer@nmr.mgh.harvard.edu

127 participants
198 discussions

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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Re: [Freesurfer] Freesurfer Digest, Vol 150, Issue 14
by Caroline Beelen 12 Aug '16

12 Aug '16

The error is: "Mapping unhit to unknown. Found 137851 unhit vertices". The file is made, but when trying to select it from the annotation tab in Freeview, Freeview crashes too. Regards, Caroline -----Oorspronkelijk bericht----- Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens freesurfer-request(a)nmr.mgh.harvard.edu Verzonden: donderdag 11 augustus 2016 18:00 Aan: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Freesurfer Digest, Vol 150, Issue 14 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. aseg.stats data output (shi yao wang) 2. mri_glmfit-sim problem (miracle ozzoude) 3. Re: mri_glmfit-sim problem (miracle ozzoude) 4. Re: Registration of low-resolution EPI time series to CVS MNI (avoiding resampling) (Douglas N Greve) 5. Re: resample structural ROI in functional space? (Douglas N Greve) 6. Re: query about the "normal range" in aseg.stats (Douglas N Greve) 7. Re: aseg.stats data output (Douglas N Greve) 8. Re: Problems with QDEC (Douglas N Greve) 9. Re: group analysis/ region of interest (ROI) approach (Douglas N Greve) 10. Re: Inquiries about QDEC inflated surface (Douglas N Greve) 11. Re: FS V6.0 GTM PVC ROI definition (Douglas N Greve) 12. Re: Fw: Running recon-all with T1 and FLAIR (Douglas N Greve) 13. Re: myaparc (Douglas N Greve) 14. Re: Qdec Generate Stats Data Table Error (Douglas N Greve) 15. Re: bbregister problem in FS5.1 (Douglas N Greve) 16. Re: Error with qdec (Douglas N Greve) 17. Re: Assessing local correlations across 2 modalities (Douglas N Greve) 18. Re: FS V6.0 GTM PVC ROI definition (Pradeep) 19. Re: FS V6.0 GTM PVC ROI definition (Douglas N Greve) 20. Re: Retinotopy questions (Douglas N Greve) 21. how to run correlation analysis between cortical thickness and cognitive function (Liu Y) 22. Re: how to run correlation analysis between cortical thickness and cognitive function (Douglas N Greve) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 Aug 2016 12:38:45 -0400 From: shi yao wang <wangshiyao2009(a)gmail.com> Subject: [Freesurfer] aseg.stats data output To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CA+rJNW_0aSv=AtUCFtKM=BV_7iQZZL+AGFAC-wWct5VeAxr8AA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear FS experts: How can I only out put the volume value in the aseg.stats file? I applied following command: but it will produce a table with lots of values such as brainsegvol, brainsegvolnotvent, which I donot want to use. thanks asegstats2table --subjects 004 021 040 067 080 092 \ --segno 11 17 18 \ --tablefile aseg.vol.table

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Re: [Freesurfer] qdec error
by Jasinska, Kaja 12 Aug '16

12 Aug '16

Hello, When I'm loading qdec, I get the following error messages. Can you please help. Thanks. Kaja ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 405 vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 405 vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 405 vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 612 vtkXOpenGLRenderWindow (0x7084e40): GLX not found. Aborting. -- --- Kaja K. Jasinska, Ph.D. Post-Doctoral Research Associate Haskins Laboratories 300 George Street Suite 900 New Haven, CT 06511 USA: 203-865-6163 ext 315 Cote d’Ivoire: (+225) 77 62 42 28 Skype: kaja.jasinska kaja.jasinska(a)yale.edu<mailto:kaja.jasinska@yale.edu> www.haskins.yale.edu/staff/jasinska/<http://www.haskins.yale.edu/staff/jasinska/>

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Freesurfer August 2016