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30135 discussions

QA Tools, inespecific error: parse error (standard_in)
by Julio Alberto González Torre 15 Jan '16

15 Jan '16

Hi Freesurfer users, I am recently testing the QA Tools in order to identify errors, especially aseg outliers. I don''t know if this is the right place to make this question, but I followed the instructions for download, install and usage, explained on: https://surfer.nmr.mgh.harvard.edu/fswiki/QATools I installed QATools and its dependencies: ImageMagick and gwak When I run the QA Tools there is an unespected error when trying to get aseg values: Checking asegs for outliers... > Using asegLUT: aseg_output.txt > parsing arguments ... > checking parameters ... > checking logs ... > done checking logs ... > done checking parameters ... > moving previous log files to *.bak > done moving previous log files > Processing each subcortical label ... > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > ... (several times) I can't identify why this error happens, but the output text about aseg values file is empty. The snaps output is correct. Does anybody know why is this happening? Or is there any alternative to check outliers? Thanks.

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Re: [Freesurfer] recon-all issue
by Schell, Susanne 15 Jan '16

15 Jan '16

Dear Bruce, thanks for answering. What we did to transform the original dicom files in nii.gz files is the following freesurfer command: mri_convert the nii.gz files to standard oriented and cut files are the following commands in FSL: fsl swapdim <input> -z -x -y <output> robustfov -i input -r output -i -r Of course, the output files are different concerning some characteristics, but they should not differ in the segmentation produced, should they? In the files attached to my last mail, you can see just by looking at the pictures that there are some variations in the form of the brain, which souldnt be there, or am I mistaken? Thanks very much in advance Susanne Today's Topics: 1. Re: recon-all issue (Bruce Fischl) ---------------------------------------------------------------------- Message: 1 Date: Wed, 13 Jan 2016 10:59:04 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all issue To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1601131057350.21689(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Susanne can you include prior correspondance so we have some context for your emails. Certainly 2 vs. 1 and 3 will give different results since you have changed the input file. I would think think 1 and 3 would be the same, but we need to know how you did the conversion. Look at the 001.mgz in the subjects' mri/orig dir in the cases of 1 and 3 and see if they are the same (or use mri_diff) cheers Bruce On Wed, 13 Jan 2016, Schell, Susanne wrote: > > Dear Bruce, > > ? > > thanks for answering. The recon-all command lines we use is: > > ? > > recon-all ?s subjectID ?i /data/subjectID.nii.gz > > recon-all ?s subjectID -all > > ? > > The files we used are > > 1)????? DICOM files > > 2)????? nii.gz files, but standard oriented and cut > > 3)????? nii.gz files > > ? > > When we look at the output pictures, they look different (see attached > files) > > ? > > Greetings, > > Susanne > > ? > > ? > > ? > > ______________________________________ > > Susanne Schell, Dipl.-Psych. > > ? > > Sektion St?rungen der Pers?nlichkeitsentwicklung > > Klinik f?r Kinder- und Jugendpsychiatrie > > Universit?tsklinikum Heidelberg > > ? > > Tel: (+49) ? (0)6221-56 35135 > > e-mail: susanne.schell(a)med.uni-heidelberg.de > > ? > > > ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 143, Issue 19 ******************************************* 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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(no subject)
by Jasmin Alves 14 Jan '16

14 Jan '16

-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Re: [Freesurfer] FW: problem with hard coded directory (/scratch)
by Fengji Geng 14 Jan '16

14 Jan '16

Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know. we ran recon-all -all -s <subject_name> -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>. We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch. I can also send you the strace output if needed. Thank you! --------------------------------------------------------------------------------- Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <568ABBFC.5000702(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Can you give us specific examples of problem programs? On 01/04/2016 09:54 AM, Fengji Geng wrote: > Hello Bruce, > > Happy New Year! > > After we reported the error related to '/scratch' several weeks ago > (see the email attached below), we tested the newest version of > freesurfer 6.0 recently, it looks likes that a lot of "if (-e > /scratch)" have been changed to "if (-dw /scratch)". However, there > are still a lot of binaries in the bin directory that match the string > "scratch", which cause the same error that I encountered before. I am > wondering if it is possible for you to fix '/scratch' in the bin > directory. > > Thank you! ----- Fengji

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Visualizing GLM analysis error
by Myers, Peter 14 Jan '16

14 Jan '16

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Cortical reconstruction
by Mohamed Ali Bahri 14 Jan '16

14 Jan '16

Dear Freesurfer Experts, I am wondering if the cortical reconstruction is possible for the quantitative mri images (R1, MT, PD...) obtained with the multiparameter sequences . If yes which image should i use? Many thanks in advance, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri(a)ulg.ac.be

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Postdoctoral position available, Paderborn (Germany)
by Claus Reinsberger 14 Jan '16

14 Jan '16

The Institute of Sports Medicine at the University of Paderborn invites applications for a full-time Postdoctoral Position to conduct, process and analyze EEG and other neuroimaging data in the context of sports and exercise. The primary responsibility of this position includes developing novel processing and statistical analysis methods, specifically for analyzing properties and dynamics of resting state networks, in dependence of various demands and states of fatigue in sports and exercise. The start date can be immediate and the position is scheduled for three years. Applicants are expected to have finished their PhD in biomedical engineering, Computer Science, Medical Physics, Neuroscience or related disciplines with a track record of relevant publications. The project requires experience with mathematical modeling and strong programming skills in C/C++ and Matlab/Python. Proficiency with EEG analyses is essential, experience with image registration and other statistical methods for neuroimaging are welcome. We are looking for a personality with the ability to think independently and work collaboratively, paired with high communication skills and high proficiency with English language. Postdocs will have the opportunity to strengthen their scientific and professional qualifications. The teaching responsibilities amount four semester periods per week. The Institute of Sports Medicine at the University of Paderborn is the first sports medicine program in Germany under neurological leadership with a strong focus on neurophysiology in health and elite level sports. The posted position will further the unique neurophysiological profile within the new field of applied neurosciences in sports and exercise. Applications from women are particularly welcome and, in case of equal qualifications and experiences, will receive preferential treatment according to the North Rhine-Westphalian Equal Opportunities Act (LGG), unless there are preponderant reasons to give preference to another applicant. Applications from disabled people with appropriate suitability are explicitly welcome. This also applies to people with equal opportunities in accordance with the German social law SGB IX. To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV with list of publications; 3) The names of three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: Reinsberger(a)sportmed.upb.de <mailto:Reinsberger@sportmed.upb.de> Claus Reinsberger, MD PhD Department of Exercise and Health Institute of Sports Medicine University of Paderborn Warburger Str. 100 33098 Paderborn, Germany

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Re: [Freesurfer] X-inversion for b-vectors extracted via mri_convert?
by Anastasia Yendiki 13 Jan '16

13 Jan '16

Hi Emad - I wouldn't do tractography to check the gradient vectors. All you need is to look at are the principal eigenvectors of the tensors (dmri/dtifit_V1.nii.gz), displayed as lines (not just RGB map, that's less informative). If, for example, the z coordinates need to be inverted, then the eigenvectors will look wrong in the coronal and sagittal view (the two views that involve the z dimension). Hope this helps, a.y On Mon, 4 Jan 2016, Emad Ahmadi wrote: > Hi FreeSurfer Experts, > > Happy New Year! > > I am using mri_convert to extract b vectors (bvecs) from diffusion images obtained at Bay 4. Then I use TRACULA for reconstructing white-matter pathways. The shape of the reconstructed pathways are odd, so I wanted to check if the extracted bvecs are correct. > > To check if the extracted bvecs are correct, I put them in Diffusion Toolkit, did deterministic tractography, and checked the shape of the extracted nerve fibers. In the attached ppt file, the first three slides show the shape of the extracted fibers. You can see that they don’t look right. > > Then I inverted the X components of the extracted bvecs, and did the tractography again. The last three slides show the result, which look right now. > > I had the same experience with dcm2nii tool, where I had to invert the Z component of the extracted bvecs. Just wanted to see if others have hit the same problem and confirm that I should invert the X component of the bvecs extracted via mri_convert. > > I hope a wonderful new year for everyone! > Emad > > Emad Ahmadi, MD > ----------------------------------------------- > Research Fellow in Radiology > Massachusetts General Hospital > Harvard Medical School > > 25 New Chardon Street, Suite 400 > Boston, MA 02114 > Tel: 617 726 5237 > Email: emad(a)nmr.mgh.harvard.edu > >

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Trac-all -path Segmentation error
by Katherine Damme 13 Jan '16

13 Jan '16

Hello Everyone! It looks as though my prep and bedp stages completed properly, but the prep stage ends in a segmentation errror. See attached and let me know your thoughts. I would prefer not to have to redo all steps if possible! Thank you!

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Cortical thickness parcellates
by John Anderson 13 Jan '16

13 Jan '16

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