Freesurfer

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30132 discussions

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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Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files
by Nikita Nogovitsyn 12 Jun '18

12 Jun '18

External Email - Use Caution HI I would like to report to have the same issue. There were no errors in the log yet the majority of results missing right hemisphere. Attaching here the log file, or you can also access it via googledrive here: https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv Thanks Nikita

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Poor anterior temporal lobe surfaces
by Meaghan Perdue 12 Jun '18

12 Jun '18

External Email - Use Caution Hello Freesurfer experts, I tried to send this out last week, but I'm not sure whether it made it to the list. I have come across a problem with several subjects in which the pial surface fails to adequately capture the anterior temporal lobes. This occurs despite accurate brainmask and wm volumes. I have included a screen shot below, in this case, the wm surface is also affected, but this is not always the case. This is pediatric data that was acquired on a 1.5T scanner and processed in Freesurfer v 5.3. The following expert options have been employed to try to improve surface rendering: mris_make_surfaces -max_gray_at_csf_border 80 -max_csf 30 -min_gray_at_csf_border 35 Please let me know how I can solve this issue. As a second question, I've heard that segmentation and surface rendering is improved with v 6.0, and I'm wondering if subjects that have been initially run through v. 5.3 and had manual edits made can then have autorecon run through v 6.0 for improvement of surfaces? Please let me know if this would be a reliable/recommended approach to improving surfaces. Thank you, Meaghan Perdue -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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Difference between Freesurfer and Voxel Based Morphometry
by Miguel Ángel Rivas Fernández 12 Jun '18

12 Jun '18

External Email - Use Caution Hi Freesurfer developers, I´m starting in structural MRI analysis with Freesurfer and i would like to know what is the main difference between freesurfer and the voxel based morphometry approach. It is more appropiate to use a method for some specific analysis? Thanks in advance. Best, -- *Miguel Ángel Rivas Fernández*

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ExploreDTI Workshop in September 2018
by Szabolcs David 11 Jun '18

11 Jun '18

External Email - Use Caution ExploreDTI Workshop - A course on processing, analyzing, and visualizing diffusion MRI data When: 10-12 September, 2018 Where: Utrecht, Netherlands Details: http://www.exploredti.com/workshop See you soon in the early Dutch autumn ;) Best, Szabolcs

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