Freesurfer

freesurfer@nmr.mgh.harvard.edu

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linyanyan@outlook.com
by Lin Yanyan 25 Nov '19

25 Nov '19

External Email - Use Caution

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Research Scientist / Engineer 3 position at the University of Washington
by Daniel J Peterson 25 Nov '19

25 Nov '19

External Email - Use Caution The University of Washington Department of Radiology currently has an outstanding opportunity for a RESEARCH SCIENTIST ENGINEER 3. The Research Scientist/Engineer 3 contributes to the growth & success of the Department by executing the mission and vision. The Integrated Brain Imaging Center in the UW Department of Radiology is a research resource center for the interdisciplinary triangle of human MRI based imaging, cognitive neuroscience, and medicine. This is a vibrant multidisciplinary unit working on cutting edge multimodal imaging methods, interoperable software tools, and translation of these approaches to clinical populations. Reporting to the Director of the Integrated Brain Imaging Center (IBIC), this position provides specialized science and research consulting support for the IBIC Research Group within the Department of Radiology. The successful candidate will be one who thrives in a multidisciplinary environment; can maintain a cutting edge conceptual understanding of image processing methods, analysis, and interpretation; views operationalizing methods on science as an exercise in problem solving; and enjoys integrating science and methods, operationally and conceptually. The successful candidate will demonstrate a trajectory of increasing responsibility for facilitating projects requiring divergent intellectual disciplines Please see the full posting for more details: https://uwhires.admin.washington.edu/ENG/Candidates/default.cfm?szCategory=…

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Re: [Freesurfer] Is -skullstrip set by default?
by Bruce Fischl 25 Nov '19

25 Nov '19

Hi Tashrif yes, because then you can just run it by itself (as opposed to part of one of the -autorecon targets) cheers Bruce On Mon, 25 Nov 2019, Billah, Tashrif wrote: > Hi Bruce, > > Thanks for your reply. But then we wouldn't need a -skullstrip option again given it's on my > default, would we? > > Best, > Tashrif > > ------------------------------------------------------------- > > Tashrif Billah, MS > > Research Engineer > > Brigham and Women's Hospital > > Harvard Medical School > > tbillah(a)bwh.harvard.edu > > http://pnl.bwh.harvard.edu/tashrif-billah-m-s/ > > >

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Is -skullstrip set by default?
by Billah, Tashrif 25 Nov '19

25 Nov '19

With recon-all, is [-skullstrip](https://surfer.nmr.mgh.harvard.edu/fswiki/skullstrip) option set by default? I am trying to understand why there is a separate -noskullstrip option. Best, Tashrif ------------------------------------------------------------- Tashrif Billah, MS<https://www.linkedin.com/in/tashrif-billah/> Research Engineer Brigham and Women's Hospital Harvard Medical School tbillah(a)bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/

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Recon-all Error
by Meena M. Makary 22 Nov '19

22 Nov '19

External Email - Use Caution Hi, I have been getting this error with one of my subjects Recon-all. I am attaching the recon-all log file. any help would be appreciated! Meena -- — *Meena M. Makary, Ph.D.* Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> Postdoctoral Fellow | Radiology, Harvard Medical School <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> Postdoctoral Fellow | Athinoula A. Martinos Center, MGH <https://www.nmr.mgh.harvard.edu/user/4550386> Career Development and Mentoring Manager | OHBM Student and Postdoc SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449>

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freesurfer linux-ppc build
by Ryan Schneider 22 Nov '19

22 Nov '19

External Email - Use Caution Hello, Is there an available freesurfer linux power pc (Power 9) build? I can not find any information about this online. If not , I have been working on making one and would like to know if anyone else has any progress ... Thanks, Ryan Schneider Boston University

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error in preprocessing
by Muhammad Naveed Iqbal Qureshi 22 Nov '19

22 Nov '19

External Email - Use Caution Hi please see the log below. I do not understand the cause of the failure. [nqureshi@qlogin1 ~]$ recon-all -s /hpf/projects/glongoni/ADHD-200/rest.nii -subject ADHD-1 -all -hippocampal-subfields-T1 -sd /hpf/projects/glongoni/ADHD-200/ -no-isrunning Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /hpf/projects/glongoni/ADHD-200 Actual FREESURFER_HOME /hpf/tools/centos6/freesurfer/6.0.0 -rw-rw-r-- 1 nqureshi glongoni 57759 Nov 19 16:32 /hpf/projects/glongoni/ADHD-200/ADHD-1/scripts/recon-all.log Linux qlogin1.ccm.sickkids.ca 2.6.32-754.14.2.el6.x86_64 #1 SMP Tue May 14 19:35:42 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux nu_correct: Command not found. `/hpf/tools/centos6/freesurfer/6.0.0/bin/recon-all' -> `/hpf/projects/glongoni/ADHD-200/ADHD-1/scripts/recon-all.local-copy' #-------------------------------------------- #@# MotionCor Tue Nov 19 16:32:47 EST 2019 Found 1 runs /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig/001.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1 mri_convert /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz --conform mri_convert.bin /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz... mri_add_xform_to_header -c /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/transforms/talairach.xfm /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Nov 19 16:32:54 EST 2019 /hpf/projects/glongoni/ADHD-200/ADHD-1/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /hpf/projects/glongoni/ADHD-200/ADHD-1/mri /hpf/tools/centos6/freesurfer/6.0.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux qlogin1.ccm.sickkids.ca 2.6.32-754.14.2.el6.x86_64 #1 SMP Tue May 14 19:35:42 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Tue Nov 19 16:32:54 EST 2019 nu_correct: Command not found. /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.50153 /hpf/projects/glongoni/ADHD-200/ADHD-1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.50153/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.50153/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.50153/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Nov 19 16:32:55 EST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.50153/nu0.mnc ./tmp.mri_nu_correct.mni.50153/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.50153/0/ -iterations 1000 -distance 50 nu_correct: Command not found. ERROR: nu_correct Linux qlogin1.ccm.sickkids.ca 2.6.32-754.14.2.el6.x86_64 #1 SMP Tue May 14 19:35:42 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ADHD-1 exited with ERRORS at Tue Nov 19 16:32:55 EST 2019 For more details, see the log file /hpf/projects/glongoni/ADHD-200/ADHD-1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [nqureshi@qlogin1 ~]$ qsub: job 221779.qtorque2.ccm.sickkids.ca completed Regards, Naveed

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TRACULA: Too many ('s. ERROR: run list is longer than subject list
by Mazzetti, C. (Cecilia) 22 Nov '19

22 Nov '19

External Email - Use Caution Dear all, I keep having problem running -stat function within tracula with 27 subjects. If I remove some of them then the script works (up to 22 subjects). Could you please help me with this? I read in a previous post that it has to do with the FS version but even if I change it the error happens anyway... thanks so much in advance! Best, Cecilia Cecilia Mazzetti - Ph.D. Researcher Donders Centre for Cognitive Neuroimaging, room 2.257 Kapittelweg 29 | 6525 EN Nijmegen

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about to segmentation
by Halil Aziz VELİOĞLU 22 Nov '19

22 Nov '19

External Email - Use Caution Hi Mr/Mrs, I want to segment substantia nigra, nucleus ruber (red nucleus) and subthalamic nucleus in Freesurfer. These regions are not in aseg.stats file. So how can I segment these regions? Is there any pipeline or scripts? Best regard, -- Öğr. Gör. Dr. Halil Aziz Velioğlu Kognitif Sinirbilim Anabilim Dalı

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Post list
by Halil Aziz VELİOĞLU 22 Nov '19

22 Nov '19

External Email - Use Caution Hi, I want to send mail Best Öğr. Gör. Dr. Halil Aziz Velioğlu

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Freesurfer