Freesurfer July 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
160 discussions

Updating submillimeter data from 5.3 to 7.1 with -hires?
by Daniel Westfall 08 Jul '20

08 Jul '20

External Email - Use Caution Hi Everyone, I have access to two large datasets (~600 scans) that were previously collected, processed, QC'd, and manually edited where necessary in Freesurfer 5.3 with recon-all. However, the data is 0.9 mm isotropic collected in a 3T scanner. I am attempting to decide if the cost/benefit is worth switching the pipeline to Freesurfer 7.1 with the -hires flag? The processing time is not the issue, mainly redoing QC and manual corrections is the concern. 1. To publish 0.9 isotropic is it necessary to use the -hires pipeline? 2. Is it appropriate to apply corrections calculated in the Freesurfer 5.3 standard pipeline to Freesurfer 7.1 -hires (and double check). Or do the manual QCs need to be completed from the ground up? 3. With the other 2 questions in mind, is it better to just go ahead and convert the data to Freesurfer 7.1 -hires? Thank you, Daniel

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Question about 3T images and brain atlas compatibility
by Hye Min Shin 08 Jul '20

08 Jul '20

External Email - Use Caution Hello, I wanted to extract brain morphometry data (cortical thickness, surface areas, volume, etc) using PALS-B12 atlas. I have some 3T MRI images that I have preprocessed using Freesurfer 3T flag. I am wondering if it would be ok to extract MRI data from 3T images on atlases such as PALS-B12. How do we know whether certain atlases are insensitive to field strength? Best, Julia Shin

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Mapping labels from left hemisphere to right hemisphere in fsaverage space
by Yash Patel 08 Jul '20

08 Jul '20

External Email - Use Caution Hi all, I have manually drawn roi onto fsaverage space on the left hemisphere. Is there a way to transfer these labels to the right? The end goal is to extract cortical measures from labels in both hemispheres and then will be averaged for further analysis. Not interested in asymmetry. Thank you for you advice, Yash Get Outlook for iOS<https://aka.ms/o0ukef>

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Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
by Iglesias Gonzalez, Juan E. 08 Jul '20

08 Jul '20

Dear Jenna, 1.Manually editing aseg.mgz fixes the initialization (super important). 2.Manually editing wmparc.mgz fixes the intensity priors (less important, but still important) If it’s only 1 subject in a bigger study, I’d probably call it a QC fail and leave it out. If it’s a single case you’re very interested in, I would edit both aseg.mgz and wmparc.mgz (you can copy the hippocampus from one into the other, but you still need to fix the surrounding labels). Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Jenna Katherine Blujus <jkblujus(a)uwm.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, July 7, 2020 at 16:24 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution Hi Experts, I ran the hippocampal subfield segmentation protocol using a T2 image that does not cover the whole brain in Freesurfer v6.0. I noticed that the alignment of the ?h.hippoSfLabels-T2.v10 output to the anatomical boundaries of the hippocampus in some of my subjects is off. For example, the left hippocampal subfield segmentation in one subject is superior and medial to the hippocampus. I checked the aseg.presurf file (since I am using v6.0) and indeed the whole left hippocampus is off. I saw in a previous thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23942.html) that it was suggested to edit the hippocampal segmentation within the aseg file to potentially improve alignment of the subfield segmentation. However, a more recent post (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54543.html) stated that both the wmparc.mgz and aseg.mgz files would need to be edited and that this was not recommended. Do you have any recommendations on how to move forward? I did edit the hippocampal segmentation within the aseg.presurf file in one of my subjects and reran the subfield segmentation command which substantially improved the output (i.e., it overlays on the hippocampus after correction). Would you suggest that I continue with editing the aseg using previously published protocols on segmenting the hippocampus by hand or would you recommend something else? Thanks in advance! Jenna

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Atlas question
by Sara Lyn 08 Jul '20

08 Jul '20

External Email - Use Caution Hi FS developers I'm doing an ROI analysis with data data and was wondering if there exists a merged Freesurfer white matter parcellation and Johns Hopkins University white matter label atlas. If yes what is it called and where can I find it? I am trying to label the mean FA skeleton mao with this merged atlas and then deproject it to subjects native space. Thank you

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Occasionally aparc+aseg is in different orientation to input
by Ian 08 Jul '20

08 Jul '20

External Email - Use Caution Hi Freesurfers. I have a very strange problem - out of several thousand scans I've run recon-all on, some give the output in an orientation different to the input. The input here is: And the output is: I always run it in the same way... can you shine a light on what I may be missing? Ian

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bbregister using freesurfer v7
by Ellen Ji 08 Jul '20

08 Jul '20

External Email - Use Caution Dear experts, I am running bbregister and have a couple questions: 1) I am using freesurfer version 7. My understanding is that I do not need any --init argument anymore, and without it, by default it uses init-coreg. Could you confirm this? (I tested the below and it seemed fine) bbregister --s subject1 --mov $dtipath/subject1/data.nii.gz --dti --reg mri/register.dat 2) A colleague performed recon-all using freesurfer v6. Is it ok if I use bbregister on these subjects using freesurfer v7 or should I install v6? Many thanks for your input! Ellen Ji, PhD Postdoctoral researcher ***** Individual Differences in Psychosis (IDP) Lab Psychiatric University Hospital University of Zürich ellen.ji(a)bli.uzh.ch

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Problem with skull strip & general beginner questions
by Nils Böer 07 Jul '20

07 Jul '20

External Email - Use Caution Hello everyone, I hope you can help me with my little problem I encountered after manually editing the skull strip. Because my internet provider crashed I'm unable to upload the log file right now and writing this from my phone. For context: I'm analyzing data with freesurfer 6.0 because the data sets already went through the recon-all process some months ago with freesurfer 6.0. I just got the data sets and my first step was to manually edit bad skull strips using tkmedit. This worked fine but after I finished and saved the data set I wanted to run: recon-all -autorecon-pial -subjid P_01 This stopped with errors and at the bott of the log i found this note which probably led to the crash: MghRead(/usr/local/freesurfer/subjects/P_01/MRI/../MRI/asset.presurf.mgz, -1): could not open file I looked into the folder and can't even find this file. Did I miss a step I have to do before or can this be due to getting the data after running recon-all on a different PC? My pre-processing pipeline looks like this (keep in mind I already get the data after recon-all was completed): 1. Skull Strip (either manually or using gcut depending on data quality) 2. Checking surfaces visually and talairach transforms if needed 3. White matter intensity normalization. Do I need to change the order here or am I missing something completely? I'm new to freesurfer and have to get into it myself. The broad tutorials online help but it's hard to check what I have to do in which order and how. If you have other guides I can check this would be an incredible help. Thanks for the help and sorry for the long email, I really appreciate every tip. Best regards, Nils

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The European Neuroscience Institute in Göttingen (ENI-G) Germany announces positions for Group Leaders (m/f/d)
by Caspar M. Schwiedrzik 07 Jul '20

07 Jul '20

External Email - Use Caution The European Neuroscience Institute in Göttingen (ENI-G) Germany announces positions for Group Leaders (m/f/d) - Limitation: fixed-term - Working period: full-time - Tariff: salary according to TV-L - Announcement published on 06.07.2020 - Vacancy from 01.01.2021 - Application deadline: 31.08.2020 The ENI-G, a joint initiative between the University Medical Center Göttingen and the Max-Planck-Society, provides an exceptional environment for excellent young researchers in the neurosciences. *We seek:* Applicants with an outstanding record of research in neuroscience. Topics range from molecular and cellular physiology, neuronal circuit analysis, imaging (at all scales), to computational and cognitive neuroscience. Current work at the ENI-G focuses on physiology, sensory processing and plasticity in multiple species, from invertebrates to humans. Research that complements these already established topics, including computational approaches at the ENI-G is also welcome. *We offer:* Group leaders a maximal amount of independence while also providing the support necessary to build up a new research program. ENI-G will provide office and laboratory space as well as a generous start-up. State of the art equipment, including dedicated microscopy infrastructure, animal facilities, a precision workshop, IT and administrative support are available in house. Unparalleled opportunities for scientific collaboration and interaction exist within the Göttingen Research Campus, including the University of Göttingen and its Medical School, three Max Planck Institutes (Biophysical Chemistry, Experimental Medicine, and Dynamics and Self Organization), the German Primate Center and the Bernstein Center for Computational Neuroscience. We will work closely with the recently established Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (https://mbexc.de/en/)" as well as the newly starting Heart and Brain Center Göttingen. In addition to the excellent research environment that ENI-G provides, its independent group leaders can benefit from the resources and funding opportunities offered by the Collaborative Research Centers (CRC / SFB) within the Göttingen Neuroscience community. The ENI-G also houses the distinguished graduate program ‘IMPRS Neurosciences’, facilitating interactions with excellent students and providing opportunities for teaching. You will have an experienced mentor by your side, receive broad administrative support, professional leadership training, and help with relocation and establishing a life in Germany, including visa application, housing, schooling, and day-care. Successful group leaders will have the opportunity to obtain a permanent position after a two step internal and external evaluation. *We look forward to:* Applications from outstanding researchers who are enthusiastic about pursuing an independent research program in an environment that supports cutting edge research. The successful candidate is expected to develop a vigorous research program with a Ph.D. received within the last five years. Relevant research training and outstanding research reflected by high-impact publications are a prerequisite for consideration. The applicant is expected to acquire competitive third-party funding, and eligibility for ERC Starting Grant / DFG Emmy Noether level funding (or comparable) is a requirement. Details about funding opportunities can be found at http://www.eni-g.de/career/group-leader. Interested candidates should submit their curriculum vitae and record of publications highlighting their 3-5 most significant publications, as well as a research statement (3-5 pages), and a copy of their PhD degree, preferably in one pdf. Application deadline: 31 August 2020. Women are especially encouraged to apply. Applicants with disabilities and equal qualifications will be given preferential treatment. We look forward to receiving your application by *31.08.2020*: University Medical Center Göttingen European Neuroscience Institute Göttingen Christiane Becker Administration Manager Grisebachstr. 5 37077 Göttingen Tel.: 0551/39-61300 Fax: 0551/39-61399 E-Mail: c.becker(a)eni-g.de Web: http://www.eni-g.de/index.php?id=groupleader Please send your application only via e-mail as a PDF-file. Travel and application fees cannot be refunded or transferred. https://www.umg.eu/karriere/stellenangebote/stellenanzeigen-detail/?jobId=3…

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mris_convert error
by Mason Wells 07 Jul '20

07 Jul '20

External Email - Use Caution Hi Experts, I am using mris_convert to convert native FreeSurfer surf files (inflated, pial and white) to GIFTI files. However, when I view them in Freeview, there seems to be a misalignment/error (attached). The commands I ran followed this structure: Mris_convert lh.inflated lh.inflated.surf.gii Any help would be great. Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Freesurfer July 2020