Freesurfer June 2018

freesurfer@nmr.mgh.harvard.edu

105 participants
154 discussions

Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease
by Arnaud Boré 13 Jun '18

13 Jun '18

External Email - Use Caution *Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease* We are looking to recruit a post-doctoral fellow in Dr. Julien Doyon’s *Motor Learning and Plasticity Laboratory*, at McGill University. The suitable candidate will join a team of post-doctoral fellows and PhD students who are conducting neuroimaging research in motor learning, both fundamental and clinical. For the current job opening, we seek to recruit a post-doctoral fellow who will *conduct neuroimaging and behavioral studies on healthy individuals and Parkinson’s Disease (PD) patients*. These studies are part of a research program aiming to characterize motor learning related plasticity in both brain and spinal cord, as well as to identify neuronal correlates of early stages of PD at both spinal and supra-spinal levels. The position is based at the Montreal Neurological Institute (MNI). The ideal candidate is expected to take the lead in regards to the methodological aspects of the study, addressing specifically the challenges related to the functional neuroimaging of the spinal cord, and to the analysis of complex data sets. The fellow will be involved in all stages of the research projects, from experimental design to data analysis and manuscript writing. The following requirements are mandatory: - PhD degree in neuroscience or a related field; - Experience with functional neuroimaging in human participants and with neuroimaging data analysis techniques and software (i.e. SPM, FSL or similar); - Ability to work independently and to collaborate with other team members; - Excellent organizational and social skills, especially when dealing with patient participants; - Established publication record attesting the above-mentioned requirements; - Good English proficiency (especially scientific writing and oral communication). The following requirements are assets: - Experience with spinal cord imaging; - Experience with multivariate data analysis approaches as implemented in established neuroimaging data analysis software; - Good proficiency with programming (such as Python or Matlab); - French proficiency; - Research experience with PD patients (or other movement-related disorders); - Availability to start as soon as possible. If you are interested in this position, please send your CV, a cover letter and the contact information of two individuals who can provide references at the following e-mail address: *francine.belanger(a)mcgill.ca <francine.belanger(a)criugm.qc.ca>*

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Re: [Freesurfer] hippocampus subfields and manual editing
by Iglesias Gonzalez, Eugenio 13 Jun '18

13 Jun '18

External Email - Use Caution Hi Lara, A little trick you can do (it shouldn’t be too hard to implement in Matlab with the functions in $FREESURFER_HOME/matlab) For each subject: 1. make a copy of aseg.mgz 2. create a binary mask for your edited hippocampi. 3. in aseg.mgz, replace each voxel labeled as hippo by the label of the closest, non-hippocampal structure. 4. Paint your hippocampi from step 2 on the hippocampal-less aseg. I hope this helps, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 13/06/2018, 17:18, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Lara Foland-Ross" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of lfoland(a)stanford.edu> wrote: External Email - Use Caution Hello, I am running an analysis of hippocampus volume on a set of T1-weighted scans with 1mm^3 isotropic resolution. Due to flow and other artifacts, a moderate degree of manual editing was required to correct the boundaries of each subject's hippocampus. Final volumes of manually edited hippocampi were submitted to a repeated measures ANOVA which showed a significant main effect of diagnosis on the overall size of this structure (controlling for age and TBV). We recently submitted this paper and just received a request from a reviewer that asked that we run a subfield analysis on these data to better understand the regions driving this overall effect. What I'd like to know is: would the subfield approach *not* be recommended on this dataset considering that artifacts necessitated a good deal of manual intervention for the entire region? Second, if it a subfield approach *is* okay to run on these data, how can I feed in my manually edited volumes to ensure that the corrected segmentations of the entire hippocampus is used during subfield creation? thanks very much in advance! Lara Lara Foland-Ross, Ph.D. Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 _______________________________________________ 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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hippocampus subfields and manual editing
by Lara Foland-Ross 13 Jun '18

13 Jun '18

External Email - Use Caution Hello, I am running an analysis of hippocampus volume on a set of T1-weighted scans with 1mm^3 isotropic resolution. Due to flow and other artifacts, a moderate degree of manual editing was required to correct the boundaries of each subject's hippocampus. Final volumes of manually edited hippocampi were submitted to a repeated measures ANOVA which showed a significant main effect of diagnosis on the overall size of this structure (controlling for age and TBV). We recently submitted this paper and just received a request from a reviewer that asked that we run a subfield analysis on these data to better understand the regions driving this overall effect. What I'd like to know is: would the subfield approach *not* be recommended on this dataset considering that artifacts necessitated a good deal of manual intervention for the entire region? Second, if it a subfield approach *is* okay to run on these data, how can I feed in my manually edited volumes to ensure that the corrected segmentations of the entire hippocampus is used during subfield creation? thanks very much in advance! Lara Lara Foland-Ross, Ph.D. Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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Group Analysis Covariates
by Hua, Jessica 13 Jun '18

13 Jun '18

External Email - Use Caution Dear Freesurfer Experts: I analyzed my data following the guidelines on the FSL Tutorial/Group Analysis page . I am trying to plot the adjusted values (covariates: age, sex, and ICV) for the significant clusters for each of my participants. I set up the contrast to test group differences. So testing whether there is a difference between groups regressing out the effects of sex, age, and ICV. Contrasts created were [1 -1 0 0 0 0 0 0] and [-1 1 0 0 0 0 0 0]. I then extracted values from this file (cache.th20.abs.sig.y.ocn.dat; i.e., the average value of each subject in each cluster) into my dataset. I believe these are the unadjusted values, correct? I calculated total volume and total surface area by multiplying these values by the total number of vertices in each cluster. To adjust for covariates, I ran a regression with the ExtractedClusterValues as the DV and Group, Sex, Age, and ICV as predictors. Looking at the output, there was no significant effect of group (p = .769; whereas in FreeSurfer the cluster-wise p < .001). Also when I plotted the predicted values adjusting for covariates, the means between the groups were very similar. Why am I getting a p = .769 when I adjust for covariates, but FreeSurfer has a cluster-wise p < .001? Or is there a way to calculate adjusted values in FreeSurfer? Best, Jessica

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dwi.ecclog file
by Daumail, Loic Jean 13 Jun '18

13 Jun '18

Hello, I have several questions regarding the dwi.ecclog file data from Tracula, using the FreeSurfer version V6.0.0. 1) Does Tracula still use eddy_correct from FSL, or was it updated with the new eddy function from FSL? 2) Are the values for each slice of dwi.ecclog relative to the first slice or to the previous slice, or to another template? is it the same for both rotation and translation values? 3) What is the coordinate system for the rotation values? Is there a way to determine the total rotation from these 9 values? Thanks, Sincerely, Loic Daumail

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Extract the entorhinal cortex as a mask
by Erik O'Hanlon 13 Jun '18

13 Jun '18

External Email - Use Caution Hi FS experts , I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it's straightforward Thanks for any advice Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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PREDOCTORAL POSITION at King's College London
by Walter Hugo Lopez Pinaya 13 Jun '18

13 Jun '18

External Email - Use Caution Dear colleagues, We are looking for a predoctoral research assistant with knowledge of neuroimaging to work on a research project involving the application of machine learning techniques to neuroanatomical data. The project will lead to the development of a practical and flexible web-based tool for measuring neuroanatomical alterations in any brain-based disorders. The successful applicant will have previous experience in the handling of multiple structural neuroimaging datasets within the same project. Previous experience of using machine learning would be considered a strength but is not a requisite. The post holder will join a multi-disciplinary team including neuroscientists, psychologists and computer scientists. This project is a collaboration between King’s College London, UK (Dr. Andrea Mechelli), the University of New Mexico, USA (Prof. Vince Calhoun) and the Universidade Federal do ABC, Brazil (Prof João Sato) and is funded by an Innovator Award from the Wellcome Trust. The post holder will be based at the Institute of Psychiatry, Psychology & Neuroscience (King’s College London). For more information, please see https://www.hirewire.co.uk/HE/1061247/MS_JobDetails.aspx?JobID=79233 Best wishes, Walter Hugo Diaz Sanz

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Missing Control Points and QATools
by Matthew Peverill 12 Jun '18

12 Jun '18

External Email - Use Caution Hello, We are finishing up manual inspection and editing of our dataset. As part of this process, we used QATools to generate QA reports. While we were running our reports the tmp/control.dat file was deleted from many of our subject directories (the brains had already been recon'd, so the corrected surfaces were not affected). The timing certainly suggests these were related, but we have no way of knowing if something else unrelated to QAtools happened that caused these files to be deleted. So two questions: 1) Has anyone else had an experience with QAtools where the control.dat file was deleted, or have any insight about why this could have happened? 2) Is the data in control.dat stored anywhere else? For example, can it be recovered from mri/ctrl_pts.mgz? We are mostly fine, but a few brains will need to have control points re-applied. Something of a shot in the dark, but we would love any suggestions. Thanks, -Matt Version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 uname -a: Linux vmpfc 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1+deb8u2 (2017-03-07) x86_64 GNU/Linux -- Matthew Peverill mrpeverill(a)gmail.com (preferred)

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tractstats2table - all tracts for multiple subjects
by Alexopoulos, Dimitrios 12 Jun '18

12 Jun '18

External Email - Use Caution Hi, For a group analysis, it possible to use 'tractstats2table' to generate a single table that contains all the tracts for multiple subjects? It's not intuitively obvious looking at the options with the 'tractstats2table' utility. Jim "The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email." ________________________________ 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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crypt_gkey = (null)
by Aaron Tanenbaum 12 Jun '18

12 Jun '18

External Email - Use Caution I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i get to the part where MRI_convert is creating the the orig001.mgz its gives me a segmentation fault. if i run this on a centos 6 system it works fine. below is the output of the program. /data/gizmo/data1/freesurfer5.3/bin/mri_convert /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm... crypt_gkey = (null) Segmentation fault (core dumped) Did I do anything wrong?

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Freesurfer June 2018