Freesurfer

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30089 discussions

Qdec+Table format issue ?????
by Dimitrios Trifonopoulos 05 Apr '18

05 Apr '18

Dear Recipient, I am a Master student new comer in FS. I am trying toi use the QDEC ti analyse some longitudinal data. Most probably my issue is related with the file format. I tried to use several text editors (mac text editor, gedit and text wrangler) however I end up in 2 different errors without be able to overcome the issue. The 1st error was: ERROR: qdec table missing correct column headers? Make sure first column is labeled 'fsid' for the time point and second column is 'fsid-base' to specify the subject tempate (base), e.g.: fsid fsid-base age me1 me 22.3 me2 me 23.2 you1 you 21.6 you2 you 22.5 Simones-iMac:subjects SLMAC14$ long_mris_slopes --qdec /Applications/freesurfer/subjects/qdec/lala copy.dat.doc --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Applications/freesurfer/subjects/ and the 2nd one was: Parsing the qdec table: /Applications/freesurfer/subjects/qdec/qdec.table.dat ERROR: qdec table /Applications/freesurfer/subjects/qdec/qdec.table.dat not found or empty? Even if I found a similar error im the forum, I didn't understand finally how this guy overcome it. I also attached you the 2 files that I used. Please answer me as soon as you are available. Thank you All the Best, Dimitris

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Re: [Freesurfer] query regarding creating an atlas from nifti volumes.
by Bruce Fischl 05 Apr '18

05 Apr '18

Hi Mageshwar gcs is a surface-based format for cortical segmentation. And it wouldn't be a conversion as much as it would be a training. If you can sample your regions onto the surface in .annot format you can use mris_ca_train to build a new gcs that you can then apply with mris_ca_label cheers Bruce On Thu, 5 Apr 2018, Mageshwar Selvakumar wrote: > Dear Bruce, > > We would like to use a probabilistic atlas built upon by us (with 170 regions) on top of the harvard > oxford atlas and would like to use this extended atlas to perform segmentation and analysis on > freesurfer. We have these 170 regions in 170 different nifti files. I would like to know if we could > use these regions in .nii or .mgz format and convert it to gcs format. > > Thank you for your help, > > > Kind regards > Mageshwar Selvakumar, M.Sc > Department of Pharmakologische Bildgebung und Bildanalyse > Friedrich Alexander Universität Erlangen Nürnberg > > Office: Fahrstr. 17, 91054 Erlangen > Phone: + 49-9131-8522898 > > > ____________________________________________________________________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of > Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Sent: Thursday, April 5, 2018 3:35 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] query regarding creating an atlas from nifti volumes. > Hi Mageshwar > > what kind of an atlas are you talking about? We have multiple atlases for > different purposes. > > cheers > Bruce > On Thu, 5 Apr 2018, Mageshwar Selvakumar wrote: > > > Dear All, > > > > I am a newbie to freesurfer and I would like to use our in-house built probabilistic atlas(each > > region as a binary mask and available as nifti files). I would like to create an atlas out of it > and > > use it for our analysis. On searching the previous mailing list I came across a discussion where > the > > volume information was converted into surface information and can be converted to labels and > > annotations but I couldn't find much documentation on creating an atlas directly from the volume > or > > surface information. It would be nice if someone can point me out if this is possible and some > > relevant information to continue on it. > > > > Thank you, > > > > Kind regards > > > > Mageshwar Selvakumar, M.Sc > > > > Department of Pharmakologische Bildgebung und Bildanalyse > > > > Friedrich Alexander Universität Erlangen Nürnberg > > > > > > Office: Fahrstr. 17, 91054 Erlangen > > > > Phone: + 49-9131-8522898 > > > > > > > > > >

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query regarding creating an atlas from nifti volumes.
by Mageshwar Selvakumar 05 Apr '18

05 Apr '18

Dear All, I am a newbie to freesurfer and I would like to use our in-house built probabilistic atlas(each region as a binary mask and available as nifti files). I would like to create an atlas out of it and use it for our analysis. On searching the previous mailing list I came across a discussion where the volume information was converted into surface information and can be converted to labels and annotations but I couldn't find much documentation on creating an atlas directly from the volume or surface information. It would be nice if someone can point me out if this is possible and some relevant information to continue on it. Thank you, Kind regards Mageshwar Selvakumar, M.Sc Department of Pharmakologische Bildgebung und Bildanalyse Friedrich Alexander Universität Erlangen Nürnberg Office: Fahrstr. 17, 91054 Erlangen Phone: + 49-9131-8522898

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Re: [Freesurfer] error rerunning recon-all (exited with ERRORS)
by Anna Daniels 05 Apr '18

05 Apr '18

Hi Douglas, thank you for the quick reply! That helped for the first hard failure. Do you have any idea what could have caused the second error message? This only happened for some subjects when rerunning recon-all with -autorecon2 -autorecon3, but always resulted in this error log: Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 Cannot allocate memory Linux node098 2.6.32-696.20.1.el6.x86_64 #1 SMP Thu Jan 25 08:47:49 CST 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 44538_T1_fs_edit exited with ERRORS at Do 29. Mär 01:28:15 CEST 2018 Attached you can find the respective recon-all.log file. Thank you! Best, Anna

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Abstract submission deadline extended - 1st International Workshop on Predictive Processing
by Sanjeev Nara 05 Apr '18

05 Apr '18

Hello Researchers, We have received request from lot of researchers to extend the deadline for abstract submission, We are happy to announce that the deadline for abstract submission for 1st International Workshop on Predictive Processing (WoPP) has been extended upto 16th April 2018. Hope to see you in San Sebastian. on behalf of Organisers Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Abstract submission deadline extended - 1st International Workshop on Predictive Processing We would like to inform you that the abstract submission deadline to PREDICTIVE PROCESSING has been extended. The new deadline is April 16th. The conference dates are June 20-22, 2018 Dear Researcher, We are happy to announce the new discussion arena fully centred on predictive processing. The Workshop on Predictive Processing (WoPP) will take place in San Sebastian (Spain) on June 20-22, 2018. The goal of the workshop is to address the role of predictive processing in cognition. Some of the crucial issues in this timely research topic are the extent to which prediction is a fundamental mechanism of brain function, the role of prediction in learning, and, how predictive processing is expressed across distinct cognitive domains. This workshop will gather experts from different fields in cognitive neuroscience including sensory processing, attention and memory, to work alongside the community of language processing, with the aim of furthering our understanding of the role of predictive processing in cognition. We invite submissions from researchers genuinely interested in discussing their data within the framework of the prediction view on neurocognition and brain functioning. The conference will include keynote speakers, regular talks, symposiums and poster sessions. Keynote speakers will be the main sources of discussion: Sophie Scott , University College London Moshe Bar , Bar-Ilan University Pascal Fries, Ernst Strüngmann Institute (ESI) Each keynote will be followed by a symposium on a related topic. Each symposium will be co-organized by two experts in the field, and will last 2 hours. Symposium organizers are Gina Kuperberg, Matt Davis, Craig Richter, Julien Vezoli, Lucia Amoruso and Ruth De Diego Balaguer. For further information please visit: http://www.bcbl.eu/events/prediction-2018/en/ We look forward to seeing you at the conference. Yours sincerely, The Organizing Committee Manuel Carreiras, Clara Martin, Nicola Molinaro & David Soto IMPORTANT DATES TO REMEMBER: Abstract submission and Registration OPEN Abstract deadline: April, 6th, 2018. Extended until April 16th, 2018. Notification of abstract acceptance : April 24th, 2018. Early registration deadline: May 11th, 2018. Online registration deadline: May 30th, 2018. Conference dates: June 20-22, 2018. BQ_BEGIN BQ_END

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MRIxfmCRS2XYZtkreg function
by Ricardo Valle 04 Apr '18

04 Apr '18

Dear Freesurfer community, I have stumbled upon a function called MRIxfmCRS2XYZtkreg in the Freesurfer source code on Github. It is used in several places but does not seem to be defined anywhere in the repository. Is it part of some external library? Would it be possible to take a look at its source? Thank you. All the best, Ruy

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Unsubscribing
by Barnali Basu 04 Apr '18

04 Apr '18

Hi , I have not used this for years, could you please take me off the mailing list? Thank you Barnali Basu Cell : 425 638 2936 Home: 206 257 0174

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which dev version for amygdala segmentation
by Anik Dar 04 Apr '18

04 Apr '18

Hi All, How do I download reqd. files / FS developmental version to run hippocampal/amygdala pipeline as described in the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… I tried downloading the el capitan version of the development version of freesurfer from the https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall and I cant find any code segmentHA_T1.sh Can anyone help, Thanks Ani

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Full-Time Research Assistant Position in Clinical Neuroscience at Ohio State University
by Herring, Elizabeth J. 04 Apr '18

04 Apr '18

Posted on behalf of Dr. Ruchika Prakash: Research Assistant Position Clinical Neuroscience Laboratory Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position, Clinical Neuroscience Laboratory<http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html> of Dr. Ruchika Prakash at the Ohio State University to assist in the general coordination and conduct of research in the Clinical Neuroscience Laboratory, including the administration of tests and/or questionnaires and the compilation of results; facilitate recruitment efforts between the laboratory and community partners for human subject payments; conduct neuropsychological assessment sessions with clinical populations; assist with data reduction and analyses, specifically analyses of neuroimaging data using openly-available software like FSL, AFNI, or SPM and programming experience in either UNIX or MATLAB; supervise undergraduate research assistants. Desired qualifications include: Bachelor's degree in a psychology or neuroscience; programming experience in either UNIX or MATLAB, as well as experience in neuroimaging data analyses; knowledge of software package, such as FSL, AFNI, or SPM. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com, under job listing #437275 and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu Lab Website: http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status.

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extracting morphometric values from co-ordinates
by Emmanuel Nwosu 04 Apr '18

04 Apr '18

Dear FreeSurfer Experts, Am wondering if there is a way to extract morphometry (cortical thickness, area, etc) values from a specific co-ordinate (talaraich, MNI, etc) of interest. Any help with this will be appreciated. Kind regards Emmanuel

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