Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Programmer/Research Tech position available at Washington University in St. Louis
by Westerhaus, Elizabeth 30 Jan '18

30 Jan '18

RESEARCH TECHNICIAN POSITION IN NEUROIMAGING POSITION SUMMARY: Applications are invited for a research technician at Washington University in St. Louis. This well-established laboratory studies the structural and functional organization of the human brain using multi-modal imaging: including magnetic resonance imaging (MRI) and positron emission tomography (PET). The primary focus of the lab is to understand how neurodegenerative diseases (especially Alzheimer’s disease) disrupt brain organization and mediates symptoms. Benefits of this position include: 1) Involvement in cutting edge research performed by a leading neuroimaging research laboratory 2) Potential to be involved as an author on manuscripts 3) Potential to present results at national and international conferences 4) Ability to attend talks and lectures in the field. Funding is guaranteed for up to 2 years. PRIMARY DUTIES AND RESPONSIBILITIES (Essential Functions): The primary responsibility of the research technician will be to archive/organize images (large multi-modal imaging datasets) and process neuroimaging data. The technician will study how disease affects the human brain by integrating large multi-modal imaging datasets and analyzing the relationship between brain imaging markers and clinical status. The technician will assist in various lab maintenance, transfer of files, database management, and organizational duties including tracking project progress, meet grant deadlines, and anticipate project needs. Qualifications: The qualified candidate should have at least a Bachelor's degree in human biology, neurosciences, psychology, bioengineering, computer sciences, or other related fields. The qualified candidate must have computer skills and knowledge of computer languages (e.g. Matlab, Python, shell scripting in CSH or BASH). The research technician must be dependable, have good attention to details, be well organized, be self-motivated, and be comfortable working as part of a team environment. Previous experience with neuroimaging data analysis programs is preferred but not required. Strong facility with statistical analyses is also desired. To apply, please send a letter of interest and CV to bances(a)wustl.edu<mailto:bances@wustl.edu>. Please arrange for three confidential letters of reference to be sent to the address below. Only applicants considered for employment will be contacted. Contact Information: Beau Ances MD, PhD Department of Neurology Washington University in Saint Louis Box 8111 660 South Euclid Ave Saint Louis, MO 63110 ****************************** Elizabeth Westerhaus MA  Clinical Research Specialist for Beau Ances MD, PhD Washington University School of Medicine Department of Neurology: Division of Infectious Disease 660 S. Euclid Ave.; Box 8111 St. Louis, MO 63110 Phone: 314-747-1125 Fax: 314-747-8427 <westerhause(a)neuro.wustl.edu<mailto:westerhause@neuro.wustl.edu>> Fed Ex or UPS Delivery: 620 S. Taylor Ave., Ste. 220 St. Louis, MO 63110 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Calculating cortex scalp distance of a region of interest
by Lucia B 30 Jan '18

30 Jan '18

Dear Freesurfer experts, I would like to calculate the mean distance from cortex to the scalp in a region of interest (the area under the stimulator), to investigate the influence of this distance on tDCS effects. A similar question was asked in the archives, and the use of mris_distance_transform was suggested. I am new to freesurfer, and I wasn't able to figure out if this approach is suitable for me and, if yes, what files I need to load in. I checked mris_distance_transform -help, yet I am still missing some parts. Could you point me to the right direction? As <label>, can I load in the ROI of the area under the scalp electrode? I tried to run the function with lh.pial and the lh.BA45.label just to see how it works, and I also have questions concenring the output: mris_distance_transform surf/lh.pial label/lh.BA45_exvivo.label unsigned lh.dist writing surface values to surf/lh.dist.w. avg = 101.288, stdev = 50.852, min = 0.206, max = 207.610 distance transform took 0.1 minutes How can I view the output file lh.dist.w.? And what do the values mean (is it by any chance already the mean distance from the surface to the label I am looking for, and if yes, what is the dimension)? Any suggestions would be highly appreciated! Many thanks! Lucia

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Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?
by Yendiki, Anastasia 29 Jan '18

29 Jan '18

As a sanity check, you can downsample one of the data sets that fail to 2mm iso, and see if it runs that way. This would tell you if it's a data size issue. ________________________________ From: Carissa Nicole Weis <cnweis(a)uwm.edu> Sent: Monday, January 29, 2018 5:53:59 PM To: Yendiki, Anastasia Subject: RE: [Freesurfer] TRACULA path segmentation fault error because of bedpostx? I went back and checked and it was just a mistake in our paperwork. All of the subjects’ data were acquired at 1x1x2 resolution, but for some reason some of the subjects would run through bedp on the first pass while others required several passes. I’ve requested additional memory on our cluster to run the subjects who stalled, but that didn’t make a difference. If you don’t see any potential issues from your end, then I’m beginning to think it could be a technical issue with our cluster perhaps it’s timing out or freezing after running for too long. I’ll look into this more to see if I can find any issues there. Do you have any other recommendations for troubleshooting at this point? Thanks, Carissa From: Yendiki, Anastasia [mailto:AYENDIKI@mgh.harvard.edu] Sent: Monday, January 29, 2018 1:54 PM To: Carissa Nicole Weis <cnweis(a)uwm.edu> Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx? The subjects that run through with no problems have 2mm isotropic resolution and the subjects that give you the segmentation fault have higher resolution? Then it sounds like a problem of insufficient memory. ________________________________ From: Carissa Nicole Weis <cnweis(a)uwm.edu<mailto:cnweis@uwm.edu>> Sent: Sunday, January 28, 2018 9:44:08 PM To: Yendiki, Anastasia Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx? My mistake. It was acquired that way. Also, after running my subjects through the -bedp step several times I’ve now only got one subject who is lingering there, but some subjects had to run 7+ times through bedp before finishing properly. I do have another dataset to analyze that was acquired with the same parameters so it’s quite possible this issue may arise again. Thanks again for your help, Carissa 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] aparc-aseg vs aseg label maps
by elisabetta_delre＠hms.harvard.edu 29 Jan '18

29 Jan '18

Hi FS team, running FS 5.3 and checking the labelmaps, there are some differences between the aseg and the aparc-aseg maps. The aparc-aseg are more inclusive. My understanding is that volumes for global measures are calculated from aseg. Could that cause problems in accuracy? Thank you so much, best, Elisabetta > > _______________________________________________ > 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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Strange Segmentation
by Maksimovskiy, Arkadiy 29 Jan '18

29 Jan '18

Dear Experts, This brain looks a little bit strange to us, and I was wondering if someone might be able to chime in about whether this is worth editing, based on the screenshots of different slices from the sagittal view.. Thank you for your expertise. -Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School [cid:image001.png@01D39915.A264E300][cid:image002.png@01D39915.A264E300][cid:image003.png@01D39915.A264E300][cid:image004.png@01D39915.A264E300][cid:image005.png@01D39915.A264E300]

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To Yendiki, Anastasia on TRACULA
by Renew Andrade 29 Jan '18

29 Jan '18

Dear Anastasia: All the output I get is the if Expression Syntax.

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strange output from lme analysis - Max r value=inf
by Valsasina Paola 29 Jan '18

29 Jan '18

Dear all I am using the lme toolbox to perform a longitudinal comparison of cortical thickness among 4 patient groups. Following the lme tutorial, I concatenated all files and I built a design matrix with following columns: -one column for intercept (all ones) -one column for time -four columns for each group (1 for subjects belonging to the group, zero otherwise) -four columns for group by time interaction I then built appropriate contrasts to test the effects of time, group and time x group effect; e.g., to test time x group interaction between group 1 and group 2, I built the following contrast: CM.C=[0 0 0 0 0 0 1 -1 0 0] However, I obtain quite strange results, because I get a lot of very small, very significant clusters of difference (having max t value = inf or -inf). Do you have any idea of the reason why I am getting this strange output? In your opinion, is there anything wrong in my design matrix or in the way I defined the contrasts? This is the first time I am trying to compare four groups in the same LME models, I previously ran LME statistics including just one or two groups, and everything ran smoothly. Please see a snapshot of my output statistic below: # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot 1 -inf 112586 0.96 -19.0 -95.2 8.3 1 lateraloccipital 2 -inf 93693 0.89 -22.0 54.4 16.4 1 rostralmiddlefrontal 3 inf 29207 0.86 -35.9 46.6 -9.9 1 parsorbitalis 4 inf 158564 0.78 -13.7 -98.8 2.3 1 lateraloccipital 5 -inf 67614 0.69 -8.3 35.1 25.4 1 superiorfrontal 6 -inf 123144 0.69 -40.3 19.5 29.8 1 caudalmiddlefrontal 7 -inf 2273 0.68 -55.6 -30.9 24.2 1 supramarginal 8 -inf 140663 0.67 -6.2 39.1 -4.4 1 rostralanteriorcingulate 9 -inf 5857 0.64 -35.5 8.6 50.8 1 caudalmiddlefrontal 10 inf 87756 0.61 -14.1 -98.2 1.7 1 lateraloccipital 11 inf 95576 0.56 -43.9 24.5 27.5 1 rostralmiddlefrontal 12 -inf 112122 0.56 -29.0 -62.8 35.9 1 inferiorparietal 13 inf 54800 0.54 -18.7 -59.3 2.6 1 lingual 14 -inf 140378 0.53 -19.0 -42.5 62.6 1 superiorparietal 15 inf 99044 0.49 -43.7 -20.0 52.6 1 postcentral 16 inf 119372 0.47 -52.1 -2.5 25.5 1 precentral 17 -inf 125951 0.47 -44.3 -55.1 12.7 1 inferiorparietal 18 inf 8776 0.46 -57.0 -2.0 11.7 1 precentral 19 inf 10137 0.44 -27.8 -49.8 -1.9 1 lingual 20 inf 20153 0.42 -6.6 13.8 29.5 1 caudalanteriorcingulate 21 -inf 19380 0.40 -61.6 -8.6 13.7 1 postcentral 22 -inf 38802 0.39 -23.9 -56.1 49.0 1 superiorparietal 23 inf 53936 0.38 -45.3 -25.9 46.7 1 postcentral 24 inf 45406 0.35 -38.8 -36.8 36.7 1 supramarginal 25 -inf 46213 0.32 -6.4 -47.6 15.7 1 isthmuscingulate 26 inf 41829 0.26 -61.1 -8.7 10.5 1 postcentral 27 -13.032 76609 0.40 -14.4 -15.8 64.7 1 precentral 28 12.272 78924 0.27 -6.0 -6.5 30.3 1 posteriorcingulate 29 -10.960 822 0.63 -51.8 -30.1 -17.2 1 inferiortemporal 30 10.326 96572 0.48 -31.7 11.6 0.5 1 insula 31 -8.509 43473 0.54 -62.2 -26.3 6.7 1 superiortemporal .. continued with a lot of significant clusters, all 1 vertex in size .. Thank you for any suggestion Best regards Paola Rispetta l'ambiente: non stampare questa mail se non ? necessario. Respect the environment: if it's not necessary, don't print this mail.

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Neurohackademy: summer school in neuroimaging and data science, July 30th - August 10th, 2018
by Ariel Rokem 29 Jan '18

29 Jan '18

We are happy to announce a call for applications to participate in Neurohackademy 2018! This two-week hands-on workshop (formerly "Neurohackweek"), held at the University of Washington eScience Institute in Seattle, July 30th - August 10th, 2018, will focus on technologies used to analyze human neuroscience data, on methods used to extract information from large datasets of publicly available data (such as the Human Connectome Project, OpenfMRI, etc.), and on tools for making human neuroscience research open and reproducible. Neurohackademy sessions in the first week will include lectures and tutorials on data science, machine learning, data visualization and data resources. The second week will be devoted to participant-directed activities: guided work on team projects, hackathon sessions, and breakout sessions on topics of interest. Instructors include Deanna Barch, Eva Dyer, Fernando Perez, Russ Poldrack, Jake Vanderplas, Gael Varoquaux, Tor Wager, and Kirstie Whitaker, among others. *For more details, see: https://neurohackademy.github.io/ <https://neurohackademy.github.io/>* We are now accepting applications to participate from trainees and researchers in different stages of their career (graduate students, postdocs, faculty, and research staff) at: https://form.jotform.com/80126067304145 Ideally, applicants should have some prior experience with neuroscience data analysis, but we welcome applications from participants with a variety of relevant backgrounds. Accepted applicants will be asked to pay a fee of $200 upon final registration. This fee will include participation in the course, accommodation in the UW dorms, and two meals a day (breakfast and lunch), for the duration of the course. A limited number of fee waivers and travel grants will be available. We encourage students with financial need and students from groups that are underrepresented in neuroimaging and data science to apply for these grants (see application form for details). *Important dates:* *March 19th: Application deadline* *April 5th: Notification of acceptance* *April 23rd: Final registration deadline* On behalf of the instructors, Ariel Rokem, University of Washington Tal Yarkoni, University of Texas, Austin

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TRACULA path segmentation fault error because of bedpostx?
by Carissa Nicole Weis 28 Jan '18

28 Jan '18

Hello all, I've been running trac-all from the command line without the configuration file since I'm not changing any defaults. I've successfully run several subjects through the trac-all -prep stage, and the -bedp stage. **Although I never got the "trac-all -bedp finished without error" prompt in the -bedp terminal output and usually just get something that says at the end: ../freesurfer_6.0/bin/bedpost_mgh: line 440: 46773 Terminated ${subjdir}.bedpostX/monitor OR it'll make it to something like... 37 slices processed 38 slices processed Queuing post processing stage 46 slices processed ...and that's as far as the output in the terminal goes. It appears all the expected files have been created in dmri.bedpostx/ so I was assuming this step had been completed. However, when I go to run the -paths step I get an error that says: Loading DWIs from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/dmri/dwi.nii.gz Loading mask from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri.bedpostX Loading b-values from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvals Loading gradients from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvecs INFO: Found 3 baseline images (b = 0) out of a total of 38 frames Segmentation fault Linux compute-026.mortimer 2.6.32-696.18.7.e16.x86_64 #1 SMP Thu Jan 4 17:31:22 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Tue Jan 9 09:34:58 CST 2018 I've checked the mask and it looks fine. I can't imagine the bvals and bvecs files should be the issue since I already made it through the -prep stage. Is it something with my bedpost outputs?? Thanks for your help! Carissa

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tracula flags
by Renew Andrade 28 Jan '18

28 Jan '18

Hello everyone! I have this problem with TRACULA. When I go to the second part of the tutorial I can´t keep going. I acknowledge that during the first part I have switch from tcsh to bash depending on errors but I’m not sure if that is normal or a mistake. The error is for example: trac-all -prep -c home/andraderenew/Downloads/freesurfer data tutorial/diffusion_tutorial/dmrirc.tutorial if: Expression Syntax Thanks!

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Freesurfer January 2018