Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

Surface Integral Questions
by Levman, Jacob 05 Apr '17

05 Apr '17

Hi FreeSurfer community, I have several questions regarding FreeSurfer's surface integral measurements. Perhaps there is a documentation page that answers these questions that someone can point me to that I haven't been able to find, or perhaps someone knows the answers to these questions off the top of their head. I understand that the negative surface integral corresponds to gyral regions and the positive surface integral corresponds to sulcal regions, but how do these differ from the Natural Surface Integral? Additionally: Integrals add up a series of underlying measurements, what is the measurement they are adding here - ie. is it a sum of local curvature measurements? What is the AreaNorm Natural Surface Integral? What is the Mean Natural Surface Integral? What is K, k1 and their differences from H, C, k2 etc. Thanks so much for your help! Jacob Levman, PhD Boston Children's Hospital Harvard Medical School

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Registration of both the brain and the "surf" files to the same template.
by Paolo 04 Apr '17

04 Apr '17

TO: freesurfer(a)nmr.mgh.harvard.edu SUBJECT: Registration of both the brain and the "surf" files to the same template. AIM: register e.g. brainmask.mgz and ?h.white for many subjects all to the same template, so that I can then take slices of brainmask.mgz and the superimposed WM surface accross subjects and compare them, confident that they are well alligned. WHAT I TRIED: used *mri_robust_register *to register all the brainmask.mgz images to a T1_1mm_template. I looked for the respective "surface" template to register the surfaces, and maybe use *mri_surf2surf*, cannot find a "surface" template that corresponds to the "T1" template. *Ideally I would like to use the same .lta transformation BOTH for the T1 image and the surface*. As I understand (?) they have a different mesh-transformation matrix. Best regards, Paolo

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Comparing LME models
by Bronwyn Overs 04 Apr '17

04 Apr '17

Hi Mailing List, If you are comparing two matlab based linear mixed effects models (vertex-wise) with the same number of random effects (e.g. model with random effect for time vs. model with random effect for age at baseline), which segmentation should you use to estimate the parameters for both models? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

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PROGRAM DIRECTOR POSITION IN COGNITIVE NEUROSCIENCE AT NSF: Application deadline May 11, 2017
by Uri Hasson 04 Apr '17

04 Apr '17

Apologies for cross-posting. The Division of Behavioral and Cognitive Sciences at the National Science Foundation is pleased to announce an opening for a Program Director in Cognitive Neuroscience. Specifics and application procedures can be found at https://www.usajobs.gov/GetJob/ViewDetails/466845000/ for a two-to-three year position and at https://www.usajobs.gov/GetJob/ViewDetails/466841200/ for a permanent position. The closing date for applications is 5/11/2017. You will need to have a Ph.D. in Cognitive Neuroscience or in a related field with relevant expertise. NSF offers the rare opportunity for scientists to join as temporary program officers for up to three years before returning to their institution. Information about the rotator program can be found at http://www.nsf.gov/about/career_opps/rotators/microsite/. For additional queries, contact Uri Hasson (uhasson(a)nsf.gov)

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Reminder: 3.5-year Postdoc Position in Social Neuroscience at Bangor University, UK
by Kami Koldewyn 04 Apr '17

04 Apr '17

Applications are invited for a 3.5-year, full time postdoctoral position with Dr. Kami Koldewyn in the Developmental Social Vision lab<https://sites.google.com/view/devsocialvislab/> in the School of Psychology at Bangor University<https://www.bangor.ac.uk/psychology/> (Wales, UK). The post is part of a European Research Council funded Starting Grant focused on Developmental Social Neuroscience. The project, ‘Becoming Social’, investigates developmental change in social perception, social learning and the social brain in late-childhood/early adolescence. The successful applicant will be the coordinator of the first major research stream of the Becoming Social project, which focuses on understanding the typical adult system and developing tasks and methods that will be applied throughout the five-year project in the longitudinal developmental streams. Methods used may include behavioural, eye-tracking and neuroimaging (e.g. fMRI, DWI) measures and the postdoctoral researcher who fills this post will be very involved, both conceptually and technically, in the design and construction of research questions and the tasks to address them. Duties will include working to develop tasks and materials that will be used across the entire project (including not only typical adults but children/adolescents aged 9-16 both with and without an Autism Spectrum Disorder). The postdoctoral researcher will be a key member of the Becoming Social team and will work closely with other team members. A PhD or equivalent in a relevant field (e.g., Psychology, Neuroscience, Cognitive Science, Biomedical Imaging/Engineering or Computer Science), as well as outstanding written and spoken communication skills are essential. In addition, this particular post requires significant technical and/or neuroimaging abilities. The successful candidate needs to be comfortable with tackling new imaging and analysis methods and have the technical chops to do so. Closing date for applications: 10th April, 2017. Proposed start date: Between May 1st and July 1st 2017 (though exact timing is flexible for the right candidate). For full details see this document: PDF of advertisement<applewebdata://8363BA95-3EFE-416C-984D-14CCBC3B24E1/goo.gl/Q4y9fM> To apply, visit: jobs.bangor.ac.uk — Job BU01403<https://goo.gl/fUQCcm> For more information or discuss eligibility please contact: Kami Koldewyn at k.koldewyn(a)bangor.ac.uk<mailto:k.koldewyn@bangor.ac.uk> Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

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Can anyone help with this error - trying to compare 2 scans in same person
by Brad Matushewski 04 Apr '17

04 Apr '17

From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Brad Matushewski Sent: March 30, 2017 2:38 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Trying to compare 2 scans from same person, 6 months apart. 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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Re: [Freesurfer] wm edits not incorporated
by Octavian Lie 04 Apr '17

04 Apr '17

Dear Bruce, > > I just transferred subject r02.tar.gz. > > Again, wm.mgz edits (all deleted voxels, no additions) are not > incorporated on reruns using any of the > recon-all -autorecon-wm -aitorecon3 > recon-all -autorecon2 -autorecon3 > recon-all -make all > > For example, the complete command line for a rerun on this particular > subject is > > recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02 > -parallel > output.txt & > > > Here are some of the edited voxels which are not excluded from the wm on > rerun: > > > -40.14, -2.67, 116.29 coronal slice 132 > 12.73, -23.67, 126.16 coronal slice 171 > 14.05, 12.33, 11.61 coronal slice 147 > > > I mention this is not the only subject where I have this problem. > Thank you for your help. > Octavian > > >

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Creating an illustration on what Freesurfer has considered to be intracranial volume
by Erik Lindberg 04 Apr '17

04 Apr '17

Dear Freesurfer experts, I would like to create an image on tissue that Freesurfer has been included into the intracranial volume calculation. Is there anyway to summarize segmentations masks so I get one mask containing all tissue that has been included into the intracranial volume? best Erik

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A question regarding LUT/Freeview
by amir hosein 04 Apr '17

04 Apr '17

Dear All, A quick question. I Want to use Freeview to display a number of brain areas (that I have chosen for some purposes) on the brain. As I have studied in this forum, it is suggested that I should create a custom Look-Up-Table in which I only keep the labels that are my target and erase others, so that when I give the Freeview a range of lables, only my target labels are displayed. So far, so good. Now, this is how I have changed part of the LUT, as an example: … 2027 ctx-rh-rostralmiddlefrontal 75 50 125 0 2028 ctx-rh-superiorfrontal 20 220 160 0 2029 ctx-rh-superiorparietal 20 180 140 0 2032 ctx-rh-frontalpole 100 0 100 0 2033 ctx-rh-temporalpole 70 70 70 0 2034 ctx-rh-transversetemporal 150 150 200 0 2035 ctx-rh-insula 255 192 32 0 … As you can see, I have omitted the labels #2030 and 2031 from my LUT. Now, I load this LUT in Freeview, and on the box on the left side I do not see these two labels, as they are already omitted. However, when I give the freeview this range 2028:2035, still the two labels of 2031 and 2031 are displayed !! I have omitted them from the list, but they still want to come! Do you think I am doing something wrong? Many thanks, Amir

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eTIV estimation on same subject over time
by Melanie Ganz 04 Apr '17

04 Apr '17

Dear list, we are currently working with some longitudinal data where we would like to measure volume changes over time and compare the cross-sectional and longitudinal stream on. When we run the cross-sectional stream and just look at changes of eTIV within subjects over a period of 6 months to a year we get 3-4 subjects out of 110 that have eTIV changes of 20-30%. I've double checked the tailarach transforms using the talairach_afd tools and also manually checked the transforms with tkregister. Everything seems to be ok. I know when using the longitudinal stream we can use the single eTIV value for volume correction, but for comparison in case of the cross-sectional stream we want to use the single time point values of eTIV. Any ideas what else I can check or is this simply noise transferred from the linear estimation of eTIV? Cheers, Mel -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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