Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

wm edits not incorporated on recon-all rerun
by Octavian Lie 01 Apr '17

01 Apr '17

Dear All, I am stuck. Several brains I segment need both wm and pial edits, typically deleting incorrectly incorporated voxels, such as dural voxels for pia, and basal temporal hyperintensity artifact or bright dural voxels included due to partial volume effects for wm. I edited brainmask.mgz or brain.finalsurfs.manedit.mgz for pia, and wm.mgz for wm. Rerunning recon-all led as expected to pial correction, however wm edits did not end up in ?h.white, despite increasingly desperate efforts and commands: recon-all -autorecon2-wm -autorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all Please advise, I could FTP one subject to you for suggestions. Again, edits here are all voxel deletions and not additions to wm.mgz. Thank you, Octavian

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display ROI mean values for FS atlas
by X K 01 Apr '17

01 Apr '17

Hi, I am doing a project with the Desikan-Killiany atlas. After some ROI analysis, I've got some values for each area. Now I want to display these values in the brain 3D space. The values are Z statistic scores, so there are both positive and negtive values (I want Z=0 to be in the middle of the color bar). In addition, I want to have a color bar about the plot. Attached please find one example data for the displaying. Please help if you have experience about this method. Thanks. Best, Xiangzhen

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Recon-all after edits
by Manuel Delgado 31 Mar '17

31 Mar '17

Dear list, There is an issue that I have been concerned about since the beginning of my FS learning, as I have found somehow contradictory information in the tutorials. Is there a way to do an only recon-all after all the edits have been made to a subject? For example, if you have edited all the possible steps (skullstrip, control points, wm and pial surface) is it possible to use all the flags for each step in one only step? Something like: recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid <subject> Or on the other hand each step needs its own recon-all with its appropriate flag? Thank you -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN

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volume parcellation
by Almarshad F. 30 Mar '17

30 Mar '17

hi can we use mris_make_face_parcellation for fMRI data? or is there any way to do random volumetric parcellation for fMRI? and if you can advise how to generate .tri file many thanks.. fati

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HCP Course 2017: Faculty and Course Schedule Available -- Register Now!
by Jennifer Elam 30 Mar '17

30 Mar '17

Faculty listings and the full schedule of covered topics <http://store.humanconnectome.org/courses/2017/exploring-the-human-connectom…> are now available for the 2017 HCP Course: "Exploring the Human Connectome" <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstore.huma…>, to be held June 19-23 at the Djavad Mowafagian Centre for Brain Health at University of British Columbia (UBC) in Vancouver, BC, Canada! The 5-day intensive course is a great opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's approach to multimodal whole brain imaging acquisition, processing, analysis, visualization, and sharing of data and results. For more info and to register visit the HCP Course 2017 website <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstore.huma…>. Don't delay, registration is limited, and the course is filling up fast! Discounted on-site UBC accommodations are available through May 17, 2017 to attendees reserving through the HCP Course room block <https://reserve.ubcconferences.com/vancouver/availability.asp?hotelCode=%2A…> . If you have any questions, please contact us at: hcpcourse@humanconnectome. org We look forward to seeing you in Vancouver! Best, 2017 HCP Course Staff Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu www.humanconnectome.org

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Re: [Freesurfer] Recon-all after edits
by Octavian Lie 30 Mar '17

30 Mar '17

Hello Bruce, I think this ties to one of my previous questions. Most of the volumes I processed need both wm and pial edits (typically deleting incorrectly added voxels for both). More recently, I was editing wm.mgz for wm and brainmask.mgz for pial. From the wiki, if changes are made for both wm/pia, one can run recon-all -autorecon2 -autorecon3 and both changes would be incorporated, however with some volumes this does not happen: pial edits are incorporated correctly, but wm edits are not, I am not sure why, event though FS6.0.0 sees edits (running recon-all with -showedits points to edits in sm.mgz as well, and those edits propagate into filled.mgz. So next, I plan editing brain.finalsurfs.manedit.mgz for pia ( it turns out one cannot edit this also for wm when that means deleting voxels for wm), wm.mgz for wm, then run -autorecon2-wm -autorecon3. Is this a strategy, and if there are alternatives, please let me know. Also, for some reason, running recon with '-make all' does not seem to work. Thank you, Octavian On Thu, Mar 30, 2017 at 8:51 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Manuel > > -autorecon2-cp runs all the steps that autorecon2-wm does so it is > redundant. If you run autorecon2-cp and autorecon3 you will get everything > (unless you edit the aseg) > > cheers > Bruce > On Thu, 30 Mar 2017, Manuel Delgado wrote: > > > Dear list, > > There is an issue that I have been concerned about since the beginning > of my > > FS learning, as I have found somehow contradictory information in the > > tutorials. Is there a way to do an only recon-all after all the edits > have > > been made to a subject? For example, if you have edited all the possible > > steps (skullstrip, control points, wm and pial surface) is it possible to > > use all the flags for each step in one only step? Something like: > > recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 > -subjid > > <subject> > > > > Or on the other hand each step needs its own recon-all with its > appropriate > > flag? > > Thank you > > > > -- > > Manuel Delgado Alvarado, MD > > Neurology Department > > Neuroimaging Unit > > Valdecilla Biomedical Research Institute, IDIVAL > > Santander, SPAIN > > > > > _______________________________________________ > 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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Re: [Freesurfer] smoothing kernel
by Trisanna Sprung-Much 30 Mar '17

30 Mar '17

thanks, Bruce - that is what I am learning. And if it was to smooth data from a sulcal probability map? A FWHM of 10 seems pretty high.... best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Mar 30, 2017 at 12:17 PM, Trisanna Sprung-Much < trisanna.sprung.much(a)gmail.com> wrote: > thanks, Bruce - that is what I am learning. And if it was to smooth data > from a sulcal probability map? A FWHM of 10 seems pretty high.... > > best > > Trisanna > > On Thu, Mar 30, 2017 at 9:45 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > >> Hi Trisanna >> >> sorry, there is no easy answer to this question. It depends on what you >> are trying to do. >> >> Bruce >> On Wed, 29 Mar 2017, Trisanna Sprung-Much wrote: >> >> > Hi there >> > I am wondering whether there is an acceptable FWHM to use to smooth >> surface >> > data (for instance, a probability map)? >> > >> > Many thanks >> > >> > Trisanna >> > -- >> > Ph.D. CandidateMcGill University >> > Integrated Program in Neuroscience >> > Psychology >> > >> > >> > >> > >> _______________________________________________ >> 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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Trying to compare 2 scans from same person, 6 months apart.
by Brad Matushewski 30 Mar '17

30 Mar '17

First scan is 005_IHD_1 Second scan is 005_IHD_1_post These were in $SUBJECTS / ihd I moved them into $SUBJECTS (i.e. no subfolder within $SUBJECTS folder). I am following this; https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing FsTutorial/LongProcessing - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing> surfer.nmr.mgh.harvard.edu Processing your data consists of three steps: First, run all your data independently (we also say cross sectionally) using "recon-all -all" (i.e. all time points for ... I ran a normal recon all on both scans first. I then ran this command: recon-all -base 005_IHD_1_base-tp 005_IHD_1 -tp 005_IHD_1_post -all and all seemed well. I then tried to run this command. recon-all -long <tpNid> <templateID> -all This is how I entered the command: recon-all -long 005_IHD_1 005_IHD_1_base -all It resulted in errors...here is the last bit of the error log: Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/rawavg.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 30 14:31:07 EDT 2017 /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri cp /usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.auto.xfm cp: cannot stat '/usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm': No such file or directory Linux bjmatush-System-Product-Name 4.4.0-51-generic #72~14.04.1-Ubuntu SMP Thu Nov 24 19:22:30 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 005_IHD_1.long.005_IHD_1_base exited with ERRORS at Thu Mar 30 14:31:07 EDT 2017 What went wrong?

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Parahippocampal subfields huge memory demands
by Ferdi van de Kamp 30 Mar '17

30 Mar '17

Hi all, I believe the website warns for high demands of memory, claiming it may take up to 10G for this processing step. However, when I run this on cluster the memory demands go up to 30G. This is still for one subject using one scan. Is this to be expected, has something changed in the processing pipeline? Eventually I want to run the longitudinal version, should I expect an increase in memory demands? Running the parahippocampal subfields on our cluster using: recon-all -s $subject -hippocampal-subfields-T1 Version: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Kind regards, Ferdi

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Open position at Boston/Children's Hospital for bilingual research assistant (Spanish-English) {Disarmed}
by Gaab, Nadine 30 Mar '17

30 Mar '17

The Gaab Lab<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.thegaablab.com_&d=C…> at Boston Children's Hospital is looking for a Research Assistants for a number of new projects examining language and reading development from infancy to adolescence. This includes subject recruitment for pediatric research studies (for English and Spanish speaking families) which will include close interaction with pediatricians in the Boston area, scheduling of pediatric research subjects, database maintenance, implementation and maintenance of analysis software; pediatric testing (including MRI/fMRI scanning of young children and infants<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.babymri.org_&d=BQMF…>) and data analyses (psychometrics, psychophysics and structural/functional magnetic imaging), stimuli design and administrative work (e.g., preparation of internal review board proposals). We are in particular looking for someone who is bilingual (English-Spanish) and who has experience with the administration of standardized tests (in English and Spanish). The position is ideal for anyone considering future graduate study in cognitive (developmental) neuroscience, developmental psychology, education, computer science, cognitive science or neuroscience. Bachelor's Degree in computer science, psychology, cognitive science, neuroscience, math, or related field required. Comfort with a heterogeneous computing environment (Linux/Unix, Mac, and Windows) as well as some programming experience preferred; knowledge of psychological experiment software (E Prime, Presentation, etc.) and/or fMRI analyses software helpful. Prior experience with infants and children would be very helpful. Spanish language knowledge is required. Demonstrable pre-existing interest in developmental psychology/ cognitive neuroscience desired; knowledge of neuroanatomy, statistics or machine learning helpful. Must be self-motivated and able to work in a fast-paced, changing environment and must like working with infants, children and families. Start date ASAP. Please first apply to Nadine.gaab(a)childrens.harvard.edu<mailto:Nadine.gaab@childrens.harvard.edu> with a cover letter and CV. "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<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gaablab.com_&d=DwMF…> Twitter: Nadine Gaab (@GaabLab)

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Freesurfer March 2017