Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

Freeview fly through frames
by Hervé Lemaitre 22 Nov '18

22 Nov '18

External Email - Use Caution Dear Freesurfer users, I want to use the "Save Movie Frames..." in freeview to go through 305 frames of an overlay on a pial surface. When a select: Fly through Frame Start number 0 End number 305 Step size 1 I click "write" and it writes only one image and stops. Thanks for you help. Freeview 2.0 Ubuntu 16.04 Hervé LEMAITRE Faculté de Médecine Université Paris-Sud 63, rue Gabriel Péri 94276 Le Kremlin-Bicêtre

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Average subject normal data base
by m s 22 Nov '18

22 Nov '18

External Email - Use Caution Hi, I am looking forward to create a normal database for daily use to compare with individual patient mr volumes. I was thinking about creating an average subject from a normal database of multiple subjects. After I have my average subject, would it be posssible and correct to compare this average recon individually to a new subjects recon, redoing all the averaging and comparing process only between this two? Thank you Mercedes

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Deadline approaching: Deadline approaching: Neuroscience data analyst (f/m) opening at ENI Göttingen, Germany (new opening)
by Caspar M. Schwiedrzik 22 Nov '18

22 Nov '18

External Email - Use Caution The European Neuroscience Institute Göttingen (Germany) is seeking a *Neuroscience data analyst (f/m) * initially limited until 31.12.2019 with extension options, full-time | salary according to TV-L The European Neuroscience Institute is looking to fill the position of a data analyst (full time). We are looking for a data analyst with interest and experience in systems neuroscience. Research at the European Neuroscience Institute ranges from molecular biology to human psychophysics and involves a range of model organisms (from drosophila to non-human primates), techniques and approaches (electrophysiology, two-photon imaging, fMRI, EEG, behavior). The data analyst will work closely with all of the various research groups at the European Neuroscience Institute, supporting research efforts, e.g., through modelling and statistical analyses of high-dimensional data, image processing, and programming/development of experiments. S/he will have the opportunity to develop and publish, e.g., analytical tools that arise from this work. - The applicant should possess a university degree (minimally M. Sc. or equivalent) in a relevant field, e.g., statistics, biostatistics, informatics, or similar. Prior experience in the field of systems neuroscience is highly desired. - The applicant should have experience in a research setting utilizing quantitative methods and statistics. The applicant shall demonstrate strong analytical skills and knowledge of novel and emerging analysis techniques is highly desired. Future/forward thinking in the area of big data analytics/informatics and applying them to contribute to the research groups’ scientific process is expected. - The applicant should be skilled in the analysis of multivariate datasets to reveal patterns and build models; conduct exploratory data analysis, and communicate with team lead/team members; identify improvements for existing data management and recommend requirements for new systems. - Contribute to replicability by making suggestions for existing data management and recommend requirements for new systems and identify potential data integrity issues. We are committed to open data/open science and appreciate interest and expertise in this area. - Utilize programming languages such as Python, Matlab and/or C++. - Good command of English is mandatory. The University Medical Center Göttingen takes flexible account of the individual design of working hours at the workplace. It is interested in implementing the wishes of its employees as far as possible. If you are interested in this job and have specific questions about working hours, please contact us. 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 * November 30th, 2018* University Medical Center Göttingen European Neuroscience Institute Göttingen Dr. Caspar Schwiedrzik Group Leader Grisebachstr. 5 37077 Göttingen Tel.: 0551/39-61371 Fax: 0551/39-61399 E-Mail: c.schwiedrzik(a)eni-g.de <+c.schwiedrzik(a)eni-g.de> Web: http://www.eni-g.de/ Please send your application only via e-mail as a PDF-file. also see: http://www.med.uni-goettingen.de/de/content/service/stellenanzeigen.php?id=…

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What is "...S_central" in Destrieux atlas?
by Christophe Destrieux 22 Nov '18

22 Nov '18

External Email - Use Caution Right See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/> , table 1 Best > > Christophe Destrieux > Laboratoire d'anatomie - Faculte de Medecine > 10, bd Tonnelle - 37032 Tours > 02 47 36 61 36 > > > > >> Le 15 nov. 2018 à 01:49, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> a écrit : >> >> S_ is for sulcus and G_ is for gyrus, so S_central is the central sulcus. I think Christophe included a table in his paper (right Christophe?) >> >> cheers >> Bruce >>> On Wed, 14 Nov 2018, Colin Birkenbihl wrote: >>> >>> External Email - Use Caution >>> Dear all, >>> I am currently working with MRI features calculated with the Destrieux atlas. >>> As an output I have features named like: >>> Vol_Right_S_Central >>> Vol_Left_G_precentral >>> or >>> Vol_Left_S_orbital-H_Shaped >>> I wanted to ask you, what these features stand for and if there is some mapping of those feature >>> names to brain region names which are clearly interpretable. >>> If not, it would be great if you could tell me what the above mentioned features refer to. >>> It would be great if you could help me. >>> Best wishes, >>> Colin

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'lh_G_Ins_lg&S_cent_ins_volume' and 'lh_G_insular_short_volume'
by Christophe Destrieux 22 Nov '18

22 Nov '18

External Email - Use Caution Hi Rujing Sorry for the late answer. These 2 labels correspond to the insula The insula is divided by the central sulcus of the insula (S_cent_ins_) into long insular gyri (G_Ins_lg) and short insular gyri (G_insular_short). Since the cortex lining the central sulcus of the insula was quite small, it has been grouped together with the the long insular gyri ( 'lh_G_Ins_lg&S_cent_ins_volume’) If you are interested in the volume of the whole insula you need to add the volumes of these two anatomical classes. For a complete list of anatomical classes and explanations on their anatomical meaning see : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/ Best Christophe Destrieux, Unité iBrain UMRS INSERM U1253, Université de Tours https://ibrain.univ-tours.fr/ <https://ibrain.univ-tours.fr/> Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > Le 21 nov. 2018 à 17:12, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> a écrit : > > you are getting very popular! > > > ---------- Forwarded message ---------- > Date: Wed, 21 Nov 2018 14:30:13 +0800 > From: charujing123 <charujing123(a)163.com> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] 'lh_G_Ins_lg&S_cent_ins_volume' and > 'lh_G_insular_short_volume' > > > External Email - Use Caution > > Hi, what is difference between and 'lh_G_insular_short_volume'. Are > these both insula? > Thanks. > Rujing > > 2018-11-21 > > ____________________________________________________________________________________________________ > charujing123 > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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How to automate recon-all command for multiple subjects
by Vivek Sharma 22 Nov '18

22 Nov '18

External Email - Use Caution Hi, I'm using freesurfer to generate head surfaces using MRI file. I want to execute recon-all command for number of subjects, but unable to run it. The script I'm using is: for i in `cat *subs.txt*` do recon-all -s $i -all -qcache done subs.txt contains the name of folder that contains .nii file. The scripts ends with the following error: ERROR: no run data found in /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to have a volume called 001.mgz in /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Please let me know how I can run recon-all for multiple subjects. Thank you. -- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015

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Corrupted T1 file (?) but segmentation look fine
by Anneliis Sartin-tarm 21 Nov '18

21 Nov '18

External Email - Use Caution Hello all, I have been running into a curious problem with a couple brains (8 out of 150 seem to have this problem) running through the recon-all pipeline. Upon loading brainmask.mgz, T1.mgz, and corresponding white matter and pial surfaces in Freeview, my colleague and I received an error that T1.mgz failed to load. Segmentation and parcellation seemed to run smoothly and accurately, however, the size of the T1.mgz file was 0. Assuming the file had been corrupted somehow (our server through which we run recon-all and store our data has tons of available memory), we reran the brains affected. Upon loading up the same re-run surfaces, T1.mgz loaded into the GUI as white, washed out voxels, displaying no brain at all. The size of this file is large, as well as all other surface and volume files. Curiously, the brainmask file seems normalized/stripped fine and surfaces displayed over the T1 look accurately segmented. I attached a screenshot displaying the T1.mgz file and surfaces that I'm referring to. I have a few concerns and questions. Because T1.mgz doesn't seem to be necessary for downstream manual editing and processing, can we proceed as normal, only displaying and using the brainmask file to make edits? Will our surface and volume metrics export properly without a usable T1 file? Lastly, any clues to how this might have occurred are welcomed. It seems like the mri_normalize step is the culprit, although the nu.mgz files corresponding to these brains seem normally sized. Best, Anneliis Sartin-Tarm Associate Research Specialist Neurocircuitry of Trauma and PTSD Study UW-Madison Dept. Psychiatry 608-262-6375

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faculty position at Stanford in Medical Imaging (fwd)
by Bruce Fischl 21 Nov '18

21 Nov '18

FYI ---------- Forwarded message ---------- Date: Wed, 21 Nov 2018 01:22:27 +0000 From: Jennifer A McNab <mcnabj(a)stanford.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: faculty position at Stanford in Medical Imaging External Email - Use Caution Hi Bruce, The Radiological Sciences Lab in Stanford Radiology has an open faculty position, and we would appreciate your help distributing this information to suitable candidates. This is a broad area search for medical imaging, as described, so we encourage all strong applicants to apply. I would be happy to answer or redirect any questions regarding this position. Cheers, Jennifer _____________________________________ Jennifer A. McNab, Ph.D., Assistant Professor Radiology, Stanford University, Lucas P286 _____________________________________

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回复： ?????? ?????? Recon-all run error
by 1013364183 21 Nov '18

21 Nov '18

External Email - Use Caution Dear Bruce, I am sorry to let you wait so long, I have some troubles in transferring the data set, but it has been solved. Now I have sent the data set to ftp. I hope you can take the time to help us deal with the data set. We have already Running this data set for a long time but did not get results, the name of the data set is data_Yujunjie.zip,. The run command and the expert file are in the attachment. Express your heartfelt thanks again！ yours yujunjie ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; 发送时间: 2018年11月18日(星期天) 晚上11:15 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] ?????? ?????? Recon-all run error Instructions on how you can upload tarred and gzipped files here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Sun, 18 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I am very sorry to bother you. We are currently experimenting with freesurfer, but I have > encountered a lot of problems during the experiment. We have three resolutions of data, the skull of > medium-resolution data can't be removed (neck can't be removed), and with high-resolution data, it > will report memory transfer errors. You said before that we can submit data sets to you, how should > we provide you with data sets? > > Thanks in advance > yours yujunjie > > ------------------ ???????? ------------------ > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > ????????: 2018??11??7??(??????) ????2:42 > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > ????: Re: [Freesurfer] ?????? Recon-all run error > > does it occur if you run it outside of recon-all? Do you have enough free > ram? If so, you can filedrop us the dataset and we can try to replicate and > fit ix. > > On Tue, 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I found the error location in the recon-all.log folder. Here is the place where it went wrong??I > > don't think it's the reason for insufficient memory.. > > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' > > This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 > > version and set the expert file, this error will occur.Do I need to step through the instructions > to > > see the problem? How should this error be solved? > > > > Thanks in advance > > > > yours yujunjie > > > > ------------------ ???????? ------------------ > > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > > ????????: 2018??11??6??(??????) ????9:40 > > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > > ????: Re: [Freesurfer] Recon-all run error > > > > that certainly looks like something is running out of ram. Can you run > > the command that failed directly on the command line and see if it works? > > Was anything else running on the machine at the time? We do report total > > and free memory at the start of the recon in the recon-all.log file > > > > cheers > > Bruce > > On Tue, > > 6 Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS, > > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the > > mri_convert > > > command is executed. The specific errors are as follows: > > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) > > > mri_convert.bin "$@" > > > ERROR: converting to minc > > > We want to know if our high resolution image is too large for freesurfer to handle, or our > > computer > > > memory (64GB running memory) is limited. > > > > > > Thanks a lot in advance! > > > yours sincerely, > > > yu junjie > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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'lh_G_Ins_lg&S_cent_ins_volume' and 'lh_G_insular_short_volume'
by charujing123 21 Nov '18

21 Nov '18

External Email - Use Caution Hi, what is difference between 'lh_G_Ins_lg&S_cent_ins_volume' and 'lh_G_insular_short_volume'. Are these both insula? Thanks. Rujing 2018-11-21 charujing123

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Freesurfer November 2018