Freesurfer

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transforming functional volumes to MNI without resampling
by David Beeler 07 May '18

07 May '18

External Email - Use Caution Hi, I'm trying to register and transform some raw functional data (108x108x72x175, 2mm iso voxels) to MNI space, while keeping the low res dimensions. I have tried: bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --init-fsl --bold mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg --no-resample --nearest mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg --no-resample And this looks pretty good, but not perfect... the functional data is oriented correctly but the brain seems to be a centimeter or two smaller in multiple dimensions, see: http://web.mit.edu/dsbeeler/www/images/bbregister-mni.png I'm not too surprised since the MNI brain is blurry and oddly round, but presumably there is a way to do this transformation more accurately. I've run mri_cvs_register for this subject using the --mni flag: mri_cvs_register --openmp 8 --mni --mov $subjID --outdir $mniDir And for other applications I use this m3z file to transform volumes between MNI orig.mgz and individual subject orig.mgz, but is there a way to use it to transform functional data to MNI space while keeping the functional dimensions? I could do: mri_vol2vol --mov funcVol --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz --reg register.dof6.lta --nearest --o template-in-anat.nii.gz mri_vol2vol --noDefM3zPath --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz --mov template-in-anat.nii.gz --m3z $mniDir/final_CVSmorph_tocvs_avg35_inMNI152.m3z --o template-in-MNI-m3z.nii.gz --nearest But not only is this unideal because it requires upsampling the functional data to 256x256x256, it also gets these funky wavy distortions: http://web.mit.edu/dsbeeler/www/images/m3z-mni.png Any thoughts are appreciated, thanks! -DB

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Re: [Freesurfer] V6 Stable OSX software error v- muflagřú9diffusionltistripjsßsssssshg kkss muflagřú9diffusibltistripuuf67uwweďxu dvvnçuc uf7a çyrucuf fDddnnn6x7uf
by Markus Gschwind 07 May '18

07 May '18

External Email - Use Caution Ûghrf7f77f7f7ef On Thu, May 3, 2018, 19:32 Matthew Grecsek <matt(a)grecsek.com> wrote: > External Email - Use Caution > > I'm using the following flags on my recon -all: -mprage -time -multistrip > -subcortseg > > and getting the following errors at this section of the log file: > > mri_watershed -rusage > /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat > -brain_atlas > /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca > transforms/talairach_with_skull.lta -h 5 T1.mgz brainmask_T1_PFH5.auto.mgz > \n > \n mri_watershed -rusage > /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat > -brain_atlas > /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca > transforms/talairach_with_skull.lta -h 10 T1.mgz > brainmask_T1_PFH10.auto.mgz \n > \n mri_watershed -rusage > /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat > -brain_atlas > /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca > transforms/talairach_with_skull.lta -h 20 T1.mgz > brainmask_T1_PFH20.auto.mgz \n > \n mri_watershed -rusage > /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat > -brain_atlas > /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca > transforms/talairach_with_skull.lta -h 30 T1.mgz > brainmask_T1_PFH30.auto.mgz \n > > mri_watershed -rusage > /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat > -brain_atlas > /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca > transforms/talairach_with_skull.lta -h 5 orig.mgz > brainmask_orig_PFH5.auto.mgz > > > Mode: Use the information of atlas (default parms, --help for > details) > Mode: Preflooding height manually specified > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > Referenced from: > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > dyld: Symbol not found: ___emutls_get_address > Referenced from: > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > [... more of same ...] > > WARNING: Some multi-skullstrip operations may have failed! > Continuing multi-skullstrip with the others... > ERROR: failure in calculating best preflood height param. > Darwin Matthews-MacBook-Air.local 17.5.0 Darwin Kernel Version 17.5.0: Mon > Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 > > recon-all -s mattmp exited with ERRORS at Thu May 3 12:57:24 EDT 2018 > > Attached is my log file for reference. Any suggestions appreciated. > > Cheers, > > -Matt > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >

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V6 Stable OSX software error - multistrip flag
by Matthew Grecsek 07 May '18

07 May '18

External Email - Use Caution I'm using the following flags on my recon -all: -mprage -time -multistrip -subcortseg and getting the following errors at this section of the log file: mri_watershed -rusage /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 5 T1.mgz brainmask_T1_PFH5.auto.mgz \n \n mri_watershed -rusage /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 10 T1.mgz brainmask_T1_PFH10.auto.mgz \n \n mri_watershed -rusage /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 20 T1.mgz brainmask_T1_PFH20.auto.mgz \n \n mri_watershed -rusage /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 30 T1.mgz brainmask_T1_PFH30.auto.mgz \n mri_watershed -rusage /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 5 orig.mgz brainmask_orig_PFH5.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib [... more of same ...] WARNING: Some multi-skullstrip operations may have failed! Continuing multi-skullstrip with the others... ERROR: failure in calculating best preflood height param. Darwin Matthews-MacBook-Air.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 recon-all -s mattmp exited with ERRORS at Thu May 3 12:57:24 EDT 2018 Attached is my log file for reference. Any suggestions appreciated. Cheers, -Matt

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Multiple Postdoctoral Scholar (Neuroimaging) and Research Assistant Positions at University of Connecticut, CT USA
by Roeland Hancock 05 May '18

05 May '18

External Email - Use Caution NIDL and brainLENS-east labs (Neurobiology of Individual Differences in Language Lab http://nidl-lab.org, PI: Roeland Hancock PhD; and Laboratory for Learning Engineering and Neural Systems http://brainlens.org, PI: Fumiko Hoeft MD PhD) at University of Connecticut’s Brain Imaging Research Center (UCONN’s BIRC) are seeking: (1) two full-time neuroimaging postdoctoral fellows, and (2) two full-time Research Coordinators. BIRC is also seeking one full-time IT staff. *TWO NEUROIMAGING POSTDOC POSITIONS @ UCONN* We are seeking two postdoctoral scholars. The postdocs will manage and execute a large-scale neuroimaging project investigating the neurobiological mechanisms underlying: (1) language, literacy and cognition in generally healthy young adults using multimodal neuroimaging techniques such as MRI, MRS and TMS (“Perturbation Postdoc”); or (2) intergenerational transmission of language and literacy in parent-offspring dyads using MRI techniques (“Intergenerational Postdoc”). In addition, the successful candidates will have the opportunity to be involved in other federally and non-federally funded-research projects in the laboratories, gain experience in grant and manuscript writing and large-scale project management, outreach and community engagement projects, and access to a wealth of archival developmental and longitudinal neuroimaging data on language and literacy. *Required qualifications:* · PhD or equivalent in cognitive and systems neurosciences, computer science, engineering, psychology or a closely related field · Computational skills, including knowledge of at least one programming language and Unix commands · Strong written and verbal communication skills · Leadership and organizational skills *Preferred qualifications:* · Exceptional skills in collecting and analyzing MRI, MRS, and/or TMS data · Experience in M/EEG · Documented history of productivity and leadership · Advanced knowledge and expertise in statistics, e.g. multivariate statistics, behavioral genetics, Bayesian and Monte Carlo methods The position will be formally advertised at a later date. In the meantime, interested candidates should email *info(a)nidl-lab.org <info(a)nidl-lab.org>* with *"[Postdoc Job (YOUR FULL NAME)]" in the subject line*. In the email they should include (a) a current CV, (b) a one-page cover letter describing qualifications, interest, career goals and which postdoc position they are interested in (refer to as *“Perturbation Postdoc/Project” *or*“Intergenerational Postdoc/Project”)*, and (c) a list of 3 potential referees with their contact information. The position can begin immediately. *Postdoctoral scholars from the lab have gone onto a range of research faculty and imaging director positions at institutions such as Stanford, Caltech, Boston College, and University of Texas.* *TWO FULL-TIME RESEARCH COORDINATOR POSITIONS @ UCONN* The Department of Psychological Sciences at the University of Connecticut seeks two highly independent and motivated full-time Research Coordinators (Research Assistant I, AAUP) to support a variety of research projects using neuroimaging and behavioral methods to study language, literacy, and cognition across the lifespan. The successful candidates will have the opportunity to be involved in federally and non-federally funded-research projects in the laboratories, gain experience in grant and manuscript writing and large-scale project management, outreach and community engagement projects, and access to a wealth of archival developmental and longitudinal neuroimaging data on language and literacy. This is a full-time, end-date position starting in July 2018, with a high likelihood of renewal contingent upon funding availability. The successful applicant with work with PI Roeland Hancock PhD, Assistant Professor of Psychological Sciences and Associate Director of BIRC at UCONN, and PI Fumiko Hoeft MD PhD, currently Professor of Psychiatry & Weill Institute of Neurosciences at UCSF, Deputy Director of UCSF Dyslexia Center, and Executive Director of a seven university UC-Stanford Precision Learning Center. She will start at UCONN as Director of BIRC and Professor of Psychological Sciences in August 2018. UCONN has outstanding resources for cognitive and systems neuroscience research, including a new state-of-the-art neuroimaging center BIRC. The laboratories have extensive local, national and international collaborations with other research groups such as UCSF, Haskins Labs, Yale, BCBL, U of Michigan, Stanford, U of British Columbia, Chinese University of Hong Kong. UCONN is centrally located in the New England area with easy access to nearby cultural centers such as New York, Boston, Providence and New Haven. *Description: * We are seeking full-time research assistants to run laboratory operations and manage research projects. The position would be situated at the UConn Storrs campus within the Department of Psychological Sciences. This is an excellent opportunity for those who are enthusiastic about learning new research skills, being involved in rapidly growing laboratories, and those considering going to graduate school. *Responsibilities may include, but are not limited to*: · Lab/Project management including hiring, IRBs, grants, meetings, and outreach events. · Data collection and management · Managing participant recruitment, outreach, advertising, and scheduling · Independently analyzing data and writing up findings or publication and/or dissemination · Other related duties as requested *Required Qualifications: * - BA/BS in Psychology, Cognitive Science, Neuroscience, or related field - Excellent organizational and interpersonal skills - Excellent spoken and written communication skills *Preferred Qualifications: * - Ability to prioritize and work independently as well as collaboratively with local and remote collaborators - Technical skills such as programming, neuroimaging data collection and analyses - Flexibility with work hours and responsibilities - Ability to travel within the New England area for outreach and data collection - Prior research experience The position will be formally advertised at a later date. In the meantime, please send your CV and a cover letter outlining your interests and future goals to *info(a)nidl-lab.org <info(a)nidl-lab.org>*with *"[RA Job (Your Full Name)]" in the subject line.*Candidates will be directed to formally apply online as next steps. Please feel free to contact us if you have any questions. *Research assistants from our lab have gone onto a range of graduate schools and programs at institutions such as Stanford University, Harvard University, Columbia University and University of California Berkeley. * *The University of Connecticut is committed to building and supporting a multicultural and diverse community of students, faculty and staff. The diversity of students, faculty and staff continues to increase, as does the number of honors students, valedictorians and salutatorians who consistently make UConn their top choice. More than 100 research centers and institutes serve the University’s teaching, research, diversity, and outreach missions, leading to UConn’s ranking as one of the nation’s top research universities. UConn’s faculty and staff are the critical link to fostering and expanding our vibrant, multicultural and diverse University community. As an Affirmative Action/Equal Employment Opportunity employer, UConn encourages applications from women, veterans, people with disabilities and members of traditionally underrepresented populations.*

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Problems at exporting recon-all outputs
by Miguel Ángel Rivas Fernández 05 May '18

05 May '18

External Email - Use Caution Hi Freesurfer developers, After having executed the recon-all in several subjects I tried to export all measures of the Destrieux atlas (area, volume, curvind, foldind, gauscurv, meancurv, thickness and thicknesstd) but I got an error because in some variables only zeros appear and however, in the other variables I did obtain values when doing the export. I had the same error in some variables when exported the subcortical segmentation (aseg.stats) and the wm (wmparc.stats). Why do some variables appear without any value? Thanks in advance, Cheers, -- *Miguel Ángel Rivas Fernández*

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Re: [Freesurfer] mri_segment-MRIcheckVolDims error
by Kambiz Tavabi 04 May '18

04 May '18

External Email - Use Caution Hi Bruce, The recon command I ran was… recon-all -subject subj -all I am attaching the log file to this email. Thanks for your help. Kambiz On May 4, 2018 at 9:01:15 AM, freesurfer-request(a)nmr.mgh.harvard.edu ( freesurfer-request(a)nmr.mgh.harvard.edu) wrote: 1. Re: mri_segment-MRIcheckVolDims error (Bruce Fischl) Hi Kambiz we need more information than this to help you. Can you send us the full recon-all command you ran and the recon-all.log? cheers Bruce ------------------------------------------------------------ Kambiz Tavabi PhD Institute for Learning & Brain Sciences 1715 Columbia Road N Portage Bay Building Box 357988 University of Washington Seattle, WA 98195-7988 Tel: 206-685-6173 ------------------------------------------------------------ *Confidentiality Notice: Because email is not secure, please be aware that we cannot guarantee the confidentiality of information sent by email. If you are not the intended recipient of this email, please notify the sender by reply email, and then destroy all copies of the message and any attachments.*

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Freeview surface annotation outline line thickness
by Kayle Sawyer 04 May '18

04 May '18

External Email - Use Caution The freeview flag "annot_outline=1" is great for viewing results for significant clusters from mri_glmfit-sim. Is there a way to make the outlines thicker? With the default thickness, the outlines are difficult to make out in a multipanel figure. (The "edgethickness=" flag specifies the slice intersection crosshair with the surface, not the annotation outline thickness.) Thanks, -Kayle

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T2 weighted images as input for recon-all command
by M Janani 04 May '18

04 May '18

External Email - Use Caution Hi Team, I have one doubt. Can I input T2 weighted images for recon-all command? Regards, Janani ::DISCLAIMER:: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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Re: [Freesurfer] Trouble getting git-annex files
by Ricardo Valle 03 May '18

03 May '18

External Email - Use Caution Hello, I need help recompiling dmri_train for Mac. It seems like the instructions in the Mac Developer’s don’t work. When I cd to the trc subdirectory and run make, I am told there is nothing to do. I tried editing the Makefile, adding bin_PROGRAMS = dmri_train, at which point I got a different error. I then uncommented some other lines in the Makefile and managed to start compiling dmri_train, but I’ve been getting a never-ending sequence of errors, essentially telling me that the compiler can’t find various dependencies (boost/program_options.h, itk*.h, etc.). I’ve tried running ./configure with various flags that disable or enable various build options, copying over .h files from other locations, adding -I <path> directives for the compiler in the Makefile, etc. etc. to no avail. Thank you, Ruy > On Apr 30, 2018, at 5:19 PM, Ricardo Valle <ruyvallem(a)gmail.com> wrote: > > Dear Freesurfer community, > > I am trying to recompile Freesurfer in order to get a binary of the latest version of dmri_train. I have been following the instructions in the Freesurfer Mac Developer’s page <https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page> and am stuck at the following: > git annex get --metadata fstags=makeinstall . > > I am attaching the output (stdout and stderr) from this command to this email. Please note that I called the git-annex repository mgh rather than datasrc. The purpose of running this is so I can run make install. > > Is there a way of recompiling only dmri_train or only the dmri_* programs? If not, do you know why git-annex might be giving me problems and how to solve this? > > Thank you, > Ruy > <fs-annex-get.txt>

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mri_segment-MRIcheckVolDims error
by Kambiz Tavabi 03 May '18

03 May '18

External Email - Use Caution Hi all, I noticed the following error message in a reconall-log concerning wm segmentation: mri_segment -keep -mprage brain.mgz wm.seg.mgz... ... ERROR: mri_segment-MRIcheckVolDims: volume1 height=336 != volume2 height=256. I looked at resulting surfaces and can't find a cause for concern, should I be concerned? I presume the volumes in question are non-conforming, could someone explain what the issue may be. Thanks in advance, Kambiz

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