Freesurfer

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by carolina.mr 05 Mar '13

05 Mar '13

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Re: [Freesurfer] A question regarding high FA values when running DTI script
by Rotem Saar 05 Mar '13

05 Mar '13

2013/3/5 Rotem Saar <saar.rotem(a)gmail.com> > Hi > > Attached is some pictures that might help ? Is this what you meant ? > Looking at this again - something is weird but I can't say what... > I can ZIP the data of one subject and send it to you but I don't feel > comfortable asking you to personally examine it... > Hopefully the upcoming course will shed some light on these problems... > > thanks > > Rotem > > 2013/2/26 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> Hi Rotem >> >> that's always a problem with FA estimation (the partial volume stuff I >> mean). It's hard to diagnose this without seeing some images. Can you send >> some of the registration? >> >> cheers >> Bruce >> >> >> >> On Tue, 26 Feb 2013, Rotem Saar wrote: >> >> Hi Bruce, >>> >>> Thanks for your answer and sorry about the delay in mine. >>> Registration seems fine, but I came up with some questions regarding it - >>> >>> 1) When testing the registration, using the "compare" button, I can see >>> both the diffusion and what is suppose to be the anatomical slices - but why >>> do the anatomical data it smoothed and doesn't look like a clear >>> anatomical image ? can this be related ? maybe i did something wrong ? >>> >>> 2) Another thing I thought about was that the corpuse-callosum values >>> are very high, but values for the ventricles are really low - so that even >>> really small shifts in the registration can bring to a situation that >>> values in the ventricles are higher than expected. Do u suggest manual >>> intervention in registration that will mainly follow the mid-sagittal >>> slice ? I don't mean ignoring the others, but mainly test the fit according >>> the >>> mid-sagittal slice. >>> >>> If u have any other ideas for why this is happening - I would appreciate >>> it if u share them with me in order to think of a solution. >>> >>> Thanks ! >>> >>> Rotem >>> >>> 2013/2/18 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> Hi Rotem >>> >>> that does sound high. Have you checked the registation between >>> your diffusion data and the anatomicals? >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 18 Feb 2013, Rotem Saar wrote: >>> >>> Hi all, >>> >>> I run into somthing that seems odd to me and wanted to >>> consult - >>> I run the following script for getting the FA values from my >>> DTI scans: >>> >>> 1) dt_recon --i /usr/local/freesurfer/** >>> subjects/FOLDER-NAME/DTI/**I00001.dcm >>> --s FOLDER-NAME --o /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI >>> --b >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/** >>> bvals.bval >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/** >>> bvecs.bvec >>> 2) tkregister2 --s fsaverage --surf white --reg >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa-**tal.nii.reg >>> --mov >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa-** >>> tal.nii >>> 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg >>> wmparc.mgz -reg >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/**register.dat >>> -overlay >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa.**nii >>> -fthresh 0.2 -fmax 1 >>> 4) mri_vol2vol --mov /usr/local/freesurfer/** >>> subjects/FOLDER-NAME/DTI/fa.**nii >>> --targ /usr/local/freesurfer/** >>> subjects/FOLDER-NAME/mri/orig.**mgz --s >>> FOLDER-NAME --interp nearest --o >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa_**FOLDER-NAME.nii >>> --reg >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/** >>> register.dat >>> 5) tkregister2 --mov >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa_**marsal.nii >>> --targ >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/mri/orig.**mgz >>> --reg >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa_** >>> FOLDER-NAME.nii.reg >>> 6) mri_segstats --seg >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/mri/**wmparc.mgz >>> --ctab >>> $FREESURFER_HOME/**FreeSurferColorLUT.txt --i >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa_**FOLDER-NAME.mask.nii >>> --sum >>> /usr/local/freesurfer/**subjects/FOLDER-NAME/stats/** >>> all_stats_fa_FOLDER-NAME >>> >>> >>> I got a table with all the FA values, for each segment, but >>> I suspect a >>> problem: I think that the values are too high (I set the >>> threshold to >>> 0.2-1), am I right ? >>> I'm attaching the table I got, and to be specific, I'm very >>> much interested >>> in the Corpus-Colosseum values, which are high (not >>> surprising) but when I >>> wanted to validate with some other structures, like the >>> "left putamen" I saw >>> 0.53 which is to my opinion too high ? >>> I would really appreciate if you can have a look at the >>> table I attached >>> here. >>> Can u guide me regarding what I can do to solve the problem >>> ? Is that any >>> way to confirm that after the mask, I am left only with >>> white matter ? >>> >>> Thanks ! >>> >>> Rotem >>> >>> >>> >>> >>> 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<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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qdec.table
by Varghese Chikku 05 Mar '13

05 Mar '13

All, I have completed base and long runs for qdec longitudinal analysis.Now I am struggling to make qdec.table.dat.How can I do this. Tx chikku

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processing 2 dti's from 1 experiment
by Jon Wieser 04 Mar '13

04 Mar '13

hello, we have acquired dti scans on a subject during a FMRI experiment. is it possible to process both dti's with tracule to get an average of the 2 dti's? If so, how do I setup the config file for this? Thanks Jon

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new tracula
by Andi Heckel 04 Mar '13

04 Mar '13

Dear Tracula Team, first, thank you very much for the new version with its many improvements ! I have dwi data (as nii.gz) that have already been unwarped and eddy-corrected, the bvector-textfiles have also been rotated accordingly. So, I guess, when I use TRACULA on these data, I simply set dob0=0, and doeddy=0 and dorotbvecs=0 to indicate that these steps have already been performed outside of tracula, correct ? (just want to be sure...) btw. is it safe to use the dmrirc config file from the previous version in the new version ? thank you very much and kind regards, andi

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question
by aurore curie 04 Mar '13

04 Mar '13

Hi I have a problem with one of the brain I am analysing... It seems like Freesurfer mixed the right and left hemisphere (see the picture enclosed)... I do not know how to fix it...I could add some control points but it will not help to distinguish between the left and right side... I will really appreciate any advice or idea about how I could fix this problem... Best regards Aurore

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Research Assistant Position in Cognitive Neuroscience Department of Neurology, School of Medicine, New York University
by Caspar M. Schwiedrzik 04 Mar '13

04 Mar '13

*[posting for colleagues, please write to them, not to me] * * * Research Assistant Position in Cognitive Neuroscience Department of Neurology, School of Medicine, New York University We are seeking a full-time Research Assistant to assist with cognitive neuroscience experiments involving human intracranial EEG. Main topics of investigation are language, memory, multisensory, brain-computer interface, seizures and others. Responsibilities include, but are not limited to, recruiting and scheduling of control subjects and patients, testing and recording from intracranial patients, maintenance of equipment, databases and files, as well as data analysis and manuscript preparation. Candidates who have experience with neuroimaging data collection and analysis are especially encouraged to apply. Other neuroimaging methods employed by the lab include fMRI and MEG. The laboratory provides a unique exposure to both basic research and clinical neuroscience. The position requires interaction with patients and hospital staff and therefore excellent verbal and interpersonal skills are required. Must be well-organized and detail oriented; extensive computer experience strongly preferred, with programming highly desirable. B.A. or B.S. required, such as in neuroscience, psychology, biology, computer science or biomedical engineering. The position is ideal for exceptional candidates seeking to pursue an advanced research degree in neuroscience or a related field. The position is available for 2-4 years and includes benefits. Start date can be immediately or later upon agreement. Please visit our web lab page for more information: http://www.med.nyu.edu/thesenlab *Please send resume and cover letter to: * Thomas Thesen, Ph.D. Assistant Professor of Neurology New York University School of Medicine thomas.thesen(a)med.nyu.edu

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Postdoctoral Research Fellowship - Oslo University Hospital
by Lars Tjelta Westlye 04 Mar '13

04 Mar '13

Applications are invited for a Postdoctoral Research Fellow position at the K.G. Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway. http://tinyurl.com/postdoc-position The fellow will take a lead role in a study funded by the Research Council of Norway investigating the acute behavioral, cognitive and brain functional (fMRI) effects of oxytocin administration, and is part of an Industry-Academia collaboration. The fellow will also be able to take an active part in several ongoing large-scale multimodal imaging genetics and psychiatry projects coordinated from the K.G. Jebsen Centre. The research will be carried out in a cross-disciplinary team in the MRI and biostatistics groups at the centre, which was recently granted Centre of Excellence Status by the Research Council of Norway, in close collaboration with OptiNose AS, an innovative biomedical company. The ideal candidate will be highly motivated, hold a PhD in psychology, neuroscience, engineering, neuroimaging, medicine or equivalent, have experience in designing and coordinating experimental research involving fMRI, and a strong background in neuroimaging analysis (FSL, FreeSurfer, SPM, Matlab etc). We offer an ambitious and exciting research environment with a strong multidisciplinary profile and excellent opportunities for academic development. A postdoctoral position in Norway is equivalent to the US position of assistant professor and is intended to prepare and qualify candidates for a research career. Salary is in the range between ltr. 57 and ltr 65 (468 400 NOK - 542 900 NOK, roughly USD 81k-95k), depending on qualifications. Pension and national health insurance is included in addition to several attractive welfare arrangements. Please address any informal enquiries to prof Ole A. Andreassen, MD, PhD (o.a.andreassen(a)medisin.uio.no) or assoc prof Lars. T. Westlye, PhD (l.t.westlye(a)psykologi.uio.no) Link to job ad and online application system: https://www.webcruiter.no/WcMain2/advertviewpublic.aspx?oppdragsnr=17166925…

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Re: [Freesurfer] New Freesurfer v5.2
by Ed Gronenschild 04 Mar '13

04 Mar '13

Hi Nick, Congratulations and thank you and the whole team (the Freesurfites) very much for your efforts. Cheers, Ed On 03 Mar, 2013, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Freesurfers, > > At long last, a new version of Freesurfer is available for download! > > For a list of what it contains, see this page: > > http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes > > To download it, see this page: > > http://surfer.nmr.mgh.harvard.edu/fswiki/Download > > And remember our home page is here: > > http://surfer.nmr.mgh.harvard.edu > > Our advice concerning your data and different freesurfer versions > is the > same: do not mix versions when processing a set of subjects in your > project. > > The v5.2 default stream (recon-all -all) does not produce > significantly > different results from the v5.1 stream, so there is no compelling > reason > to re-run the default stream on your subject data. However, v5.2 > contains quite a few new features and atlases, which you can run on > data > processed by v5.1. See ReleaseNotes page for details or email the > list: > > http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > Thank you to everyone who downloaded and tested the beta release of > v5.2. > > The Freesurfites > > > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 109, Issue 3 > ****************************************** > > > 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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gcut problem
by Isabelle Deschamps 04 Mar '13

04 Mar '13

Good morning, I tried to run the following command: recon-all -skullstrip -clean-bm -gcut -subjid S01 to remove the skull and remaining dura mater. However, for some subjects, I get the following error: ** Gcutted brain is much smaller than the mask! ** Using the mask as the output instead! I tried adjusting the wsthresh, as suggested in previous posts, but without success. Is there something else, I can try? Thank you in advance for your help, Isabelle

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Freesurfer