Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30091 discussions

[FSL] Re Orient image from AP to PA axis
by Dev vasu 21 Mar '17

21 Mar '17

Dear all, I would like to if there is any procedure to reorient the image ( flip ) from AP axis to PA , I have around 50 scans all of which are scanned in A/P axis and i would like to reorient them , kindly please let me know if there is any procedure. I tried mri_convert and orient_mri is freesurfer but i could not see any changes Thanks Vasudev

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Running recon-all with FLAIR / MRISread(../surf/lh.white.preaparc): could not open file
by Veronica Munoz 21 Mar '17

21 Mar '17

Dear all, I'm trying to add FLAIR data to a subject. I did the first ("classic") recon-all on a platform so I get the following warnings: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: current FREESURFER_HOME does not match that of previous processing. Current: /home/munoz/Documents/freesurfer Previous: /tmp/wrk/DIRAC_piXnbapilot/50587390/recon-all.sh-445574845579047/freesurfer Then recon all exits with the following error: #@# Jacobian white lh Tue Mar 21 12:25:24 CET 2017 /media/sf_C_DRIVE/Users/munoz/Documents/Stage_FLI/results/FLAIRtest/AC_005/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... MRISread(../surf/lh.white.preaparc): could not open file No such file or directory mris_jacobian: could not read surface file ../surf/lh.white.preaparc No such file or directory Linux iu-dv-464-vm.creatis.insa-lyon.fr 4.9.7-201.fc25.x86_64 #1 SMP Thu Feb 2 23:32:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Does this have something to do with my current Freesurfer version ? I don't really know what information does "preaparc" contain. Thank you for your help. Best regards, Veronica veronica.munoz(a)creatis.insa-lyon.fr <mailto:veronica.munoz.rmz@gmail.com>

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white matter volumes for frontal and temporal lobes
by Ahearn, T 21 Mar '17

21 Mar '17

Hello I need separate grey and white volumes for the frontal and temporal lobes. I have values for grey volume from the following... mri_annotation2label --subject 01 --hemi lh --lobesStrict lobar_annotation mris_anatomical_stats on the lh.lobar_annotation.annot file to generate a text file. I've also run similar to the below and now have a text file wmparc.a2009.stats. mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz mri_segstats --seg mri/wmparc.a2009s.mgz --sum stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject --surf-wm-vol --ctab $FREESURFER_HOME/WMParcStatsLUT.txt --etiv Is there a standard list of labels in this file that are used to create the frontal and temporal lobes? Thanks Trev The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.

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Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams
by Antonin Skoch 20 Mar '17

20 Mar '17

Dear David, did you use -uselongbasewmedits in your recon-all -long run? If this flag is not used, the wm edits are transfered to long from cross, not from the base. Regards, Antonin Skoch Andrew, thanks for your response. I am still not seeing the white matter edit performance that I am expecting, or that I have seen from using the cross stream on 5.3 in the past with a different dataset.I started with a new subject with two timepoints. I ran recon-all on both for the cross stream with no edits, and then ran the base. I edited the wm.mgz for the base, then ran “recon-all –autorecon2-wm –autorecon3 –base xx_base –tp xx_t1 –tp xx_t2”. I noticed the surfaces didn’t really change in the base, but I went ahead and ran the two long runs using “recon-all –all –long xx_tx xx_base” and although there are minor differences in the base and time point surfaces, the white matter edits I did on the base were largely ignored, and none of them were included in the time point long run wm.mgz files. I am tempted to try these same analyses using Linux (I am running this on OSX 10.11 currently), as I experienced a completely different response from the surface generation modules to my edits in the past when using Linux. I’m thinking this is a real long shot, but I cannot otherwise figure out why the software would be behaving so differently from my past experiences. Any thoughts? Thanks! Best, David P. Semanek, HCISPP Research Technician, Posner Lab Division of Child and Adolescent Psychiatry Columbia University Medical Center New York State Psychiatric Institute 1051 Riverside Drive, Pardes Bldg. Rm. 2424 New York, NY 10032 PH: (646) 774-5885 IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From: "Hoopes, Andrew" <ahoo...(a)mgh.harvard.edu> Date: Wednesday, March 15, 2017 at 12:47 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>, David Semanek <seman...(a)nyspi.columbia.edu> Cc: Bruce Fischl <fis...(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams Hi David Try editing the base wm.mgz first instead of editing the long and cross wm files. Rerun autorecon2-wm and autorecon3 for the base dir, then completely rerun the longitudinals. The long surfaces are initialized from the base surfaces, so this could be why your wm fixes seem to have no effect. You can find more info here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#CheatSheet<https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits> If editing the base doesn't solve the problem, you can send me the commands you ran in order and I can look into this further. best, Andrew ________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of David Semanek <seman...(a)nyspi.columbia.edu> Sent: Monday, March 13, 2017 11:55 AM To: Bruce Fischl; Freesurfer support list Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams Thanks, I have uploaded the cross and long stream processing from one subject which requires numerous white matter edits to correct defects in the white matter surfaces; the file is on the ftp server as dsemanek.zip. Both of the cross subject folders, s02_t1 and s02_t2 have had edits done to both the brainmask as well as the wm files, and autorecon2-wm and autorecon-3 have been run on them, as well as the long folder for the first time point, s02_t1.long.s02_base. It was in working with the rerun results of s02_t1.long.s02_base that I noticed the white matter surfaces after being regenerated with the edited wm.mgz did not reflect any of the edits. The easiest way to see this is to load the wm.mgz with the white matter surfaces and scroll through the slices, there are numerous areas where the contours of the white matter surfaces do not follow the voxels of the wm.mgz volume, mostly near what should be identified as hyperintense gray matter. I’m fairly certain the white matter surfaces didn’t change at all after running autorecon2-wm with the wm.mgz edits. Thanks for taking a look at our data. Best, David P. Semanek, HCISPP Research Technician, Posner Lab Division of Child and Adolescent Psychiatry Columbia University Medical Center New York State Psychiatric Institute 1051 Riverside Drive, Pardes Bldg. Rm. 2424 New York, NY 10032 PH: (646) 774-5885 IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. On 3/12/17, 4:13 PM, "Bruce Fischl" <fis...(a)nmr.mgh.harvard.edu> wrote: Hi David if you upload a subject to our ftp site and give us enough detail to replicate what you tried we will take a look cheers Bruce On Fri, 10 Mar 2017, David Semanek wrote: > > Hello, I have worked quite a bit in the past with fs 5.3 on datasets which > required a fair number of manual edits to the white matter volume in order > to correct defects in the white matter surface. Typically, these edits take > the form of removing voxels in the wm.mgz volume that have been incorrectly > identified as white matter, usually near the pial surface caused by > intensity artifacts resulting from motion. My experience in the past is that > generating the white matter surface after edits to the wm.mgz volume will > reliably change the geometry of the resulting surfaces. > > > > However, on my current dataset, 1.5T adolescent brains with pervasive motion > artifacts that do not meet the threshold for unusable data, absolutely no > intervention I have done on the wm.mgz volume has any impact at all on the > generation of the white matter surfaces. I am really very puzzled by this. > All of the files that result from wm.mgz reflect the edits, however the aseg > does not. > > > > The resulting white matter surfaces always follow the aseg white matter > definitions and never the wm.mgz edits. I feel as if there might be > something I am missing but this protocol has reliably been used to do white > matter edits in the past. I thought it may be an issue with fs 6 or the long > stream, but I have tried the same edits in 5.3, 6, long and cross streams > and nothing at all has worked. > > > > Does anyone have any suggestions, or perhaps a hint that I am overlooking > something common? > > > > Thanks,

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Postdoc position at the Ohio State University
by Zeynep Saygin 20 Mar '17

20 Mar '17

POSTDOCTORAL FELLOW, The Ohio State University, Dept. of Psychology – Saygin Lab. We seek an outstanding scientist with a recent Ph.D. in cognitive neuroscience, developmental psychology, or related area, who has experience with neuroimaging methods (MRI, fMRI, DWI, and/or functional connectivity) and who is interested in any or all of the following: understanding the functional and structural architecture of the brain, how it develops in healthy individuals, and how it changes with disorders and brain injury in both adults and children. See http://web.mit.edu/zsaygin for recent publications. The fellow will be involved in conducting and planning behavioral and neuroimaging research studies in neonates, infants, children, and adults. Proficiency in programming is necessary. This position is fully funded. Initial hire is for one year with additional years contingent on fit and progress. OSU is located in Columbus, Ohio and is home to a vibrant community of cognitive neuroscientists, computational modelers, and vision scientists in the Psychology Department and Center for Cognitive and Brain Sciences. Fellows will have access to state-of-the-art MRI and EEG facilities located inside the Psychology building. Interested individuals should contact zsaygin(a)mit.edu with a CV, names of 3 references, and a statement of research interests. -- Zeynep M. Saygin, Ph.D. MIT, Brain and Cognitive Sciences MGH, Martinos Center 43 Vassar St. 46-4141 Cambridge, MA 02139 http://web.mit.edu/zsaygin

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wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams
by David Semanek 20 Mar '17

20 Mar '17

Hello, I have worked quite a bit in the past with fs 5.3 on datasets which required a fair number of manual edits to the white matter volume in order to correct defects in the white matter surface. Typically, these edits take the form of removing voxels in the wm.mgz volume that have been incorrectly identified as white matter, usually near the pial surface caused by intensity artifacts resulting from motion. My experience in the past is that generating the white matter surface after edits to the wm.mgz volume will reliably change the geometry of the resulting surfaces. However, on my current dataset, 1.5T adolescent brains with pervasive motion artifacts that do not meet the threshold for unusable data, absolutely no intervention I have done on the wm.mgz volume has any impact at all on the generation of the white matter surfaces. I am really very puzzled by this. All of the files that result from wm.mgz reflect the edits, however the aseg does not. The resulting white matter surfaces always follow the aseg white matter definitions and never the wm.mgz edits. I feel as if there might be something I am missing but this protocol has reliably been used to do white matter edits in the past. I thought it may be an issue with fs 6 or the long stream, but I have tried the same edits in 5.3, 6, long and cross streams and nothing at all has worked. Does anyone have any suggestions, or perhaps a hint that I am overlooking something common? Thanks, David P. Semanek, HCISPP Research Technician, Posner Lab Division of Child and Adolescent Psychiatry Columbia University Medical Center New York State Psychiatric Institute 1051 Riverside Drive, Pardes Bldg. Rm. 2424 New York, NY 10032 PH: (646) 774-5885 IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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Re: [Freesurfer] Error in Reconstruction of bert samples.
by zkaufman＠nmr.mgh.harvard.edu 20 Mar '17

20 Mar '17

Thats odd. Does that file exist? What are the permissions of it? ls -l /home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz > IPL Neurosurgery has shared aâ¯OneDriveâ¯file with you. To view it, > click the link below. > > > <https://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw> > [https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]<https://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw> > > recon-all 1.log<https://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw> > > > > > Hi, > > > We have encountered a error in skull stripping process in bert sample. We > are a novice. We attached the log. > > > Command : recon-all -s bert -all > > > #@# Skull Stripping Sat Mar 18 14:58:05 IST 2017 > /home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri > > mri_watershed -rusage > /home/iplneurosurgery/Documents/freesurfer/subjects/bert/touch/rusage.mri_watershed.dat > -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas > /home/iplneurosurgery/Documents/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca > transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz > > > Keeping brain edits brainmask.auto.mgz brainmask.mgz > Mode: T1 normalized volume > Mode: Use the information of atlas (default parms, --help for > details) > mghRead(/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz, > -1): read error > > ********************************************************* > The input file is T1.mgz > The output file is brainmask.auto.mgz > No such file or directory > Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 > 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s bert exited with ERRORS at Sat Mar 18 14:58:06 IST 2017 > > freesurfer version: > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > > Platform: Cent OS 7 > > > uname -a : 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 > x86_64 x86_64 x86_64 GNU/Linux > > Any Suggestion will be appreciated. > > > Thanking you, > > > IPL Neurosurgery. > > > > Sent from Outlook<http://aka.ms/weboutlook> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freesurfer license tx
by Almarshad F. 20 Mar '17

20 Mar '17

i received the license through the email and tried to make a new text file contains the emailed licensed details .. i am confused where exactly to save it i tried to save it in the user/local/freesurfer but it show a permission error "ou do not have the permissions necessary to save the file. Please check that you typed the location correctly and try again" i am using the newest freesurfer release and the Ubuntu 16.04 I'm completely new to Linux and thanx a lot fatima PhD student

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Postdoctoral Position - Multimodal neuroimaging in dementia
by Heidi Foo 20 Mar '17

20 Mar '17

Postdoctoral research fellow positions are available in the Department of Neurology Research at the National Neuroscience Institute, Singapore. Our focus is to use neuroimaging techniques as a surrogate pathological marker to understand the underlying neurobiological basis of dementia especially in the preclinical stages. We are seeking highly motivated individuals who have extensive research experience in neuroimaging analyses (e.g. structural, diffusion, functional MRI) using FreeSurfer, Statistical Parametric Mapping, and FMRIB Software Library; and demonstrate academic excellence including publications in first-class journals and conferences. The postdoctoral candidate should have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or related fields. Good command of programming tools including Matlab, C++, Linux, and scripting are necessary to carry out the research work in this group. The candidate will support our efforts either in advancing neuroimaging analysis technologies or in neuroscience applications. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis. If interested, please email resume to Professor Nagaendran Kandiah (nagaendran.kandiah(a)singhealth.com.sg)

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Error in Reconstruction of bert samples.
by IPL Neurosurgery 20 Mar '17

20 Mar '17

IPL Neurosurgery has shared a OneDrive file with you. To view it, click the link below. <https://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw> [https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]<https://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw> recon-all 1.log<https://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw> Hi, We have encountered a error in skull stripping process in bert sample. We are a novice. We attached the log. Command : recon-all -s bert -all #@# Skull Stripping Sat Mar 18 14:58:05 IST 2017 /home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri mri_watershed -rusage /home/iplneurosurgery/Documents/freesurfer/subjects/bert/touch/rusage.mri_watershed.dat -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /home/iplneurosurgery/Documents/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) mghRead(/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz, -1): read error ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz No such file or directory Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Sat Mar 18 14:58:06 IST 2017 freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Cent OS 7 uname -a : 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Any Suggestion will be appreciated. Thanking you, IPL Neurosurgery. Sent from Outlook<http://aka.ms/weboutlook>

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