Freesurfer March 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
161 discussions

timeseries question
by Nasiriavanaki, Zahra 02 Mar '20

02 Mar '20

Hi Freesurferes I have extracted timeseries from a task fMRI using the command below: mri_segstats --i fmcpr.sm0.self.rh.nii.gz --slabel $subj rh rh.label --id 1 --avgwf-remove-mean --avgwf ./rh.txt My question is: Is the temporal drift being counted in considering that I used preprocessed data as the input? Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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recon-all failure
by Ian 02 Mar '20

02 Mar '20

External Email - Use Caution Hi all. I have a T1 scan which I run through recon-all with: recon-all -all -parallel -subjid freesurfer (after mksubjdirs etc) On my office machine, recon-all completes successfully. On a cloud machine (16GB of ram), it fails after about 4 hours. I have attached the logs - the only immediate error I can see is "Cannot find rh.white.H". Any advice would be much appreciated, thank you. Ian -- *Ian Hardingham*

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ERROR: fast_selxavg3() failed\n
by mahdiyeh khanbagi 02 Mar '20

02 Mar '20

External Email - Use Caution Dear FreeSurfer Developers, I am trying to do FSFAST analysis on Mac OS Catalina 10.15.3, and I have completed the preprocessing (preproc-sess, mkanalysis-sess and mkcontrast-sess) with no problem. When I ran the function selxavg3-sess, it proceeded somehow (-->preproc-sess done--> MATLAB opened and then was closed), but when it started running fast_selxavg3b it stopped after a while (fast_selxavg3() failed\n) with the following errors: Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 12, skipping 1 AnimalvsNonAnimal.mat Excluding 4 points Subscript indices must either be real positive integers or logicals. Error in fast_st2fir (line 118) Xfirss(ind,nthd) = wstim; Error in flac_desmat (line 58) flacnew.ev(nthev).Xfir = fast_st2fir(st,ntpssr,TER,ev.psdwin,useweight); Error in flac_customize (line 357) flacnew = flac_desmat(flacnew); Error in fast_selxavg3b (line 129) flac0 = flac_customize(flac0); Could anyone help me with this problem, please? Best Regards, Mahdiyeh

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make_average_subject
by Benjamin Ineichen 02 Mar '20

02 Mar '20

External Email - Use Caution Dear Freesurfer experts, I want to create a new standard template from my study population. For this, I thought about using make_average_subject. Thus, I run: make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003 I get an error message - ERROR: make_average_surface. Please find attached the error.log. Would be very thankful for advice! Many thanks! /Ben -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01

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Freesurfer Digest, Vol 193, Issue 3
by Faith Gunning 02 Mar '20

02 Mar '20

External Email - Use Caution Thanks, Lauren. Faith ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Monday, March 2, 2020 12:00 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Freesurfer Digest, Vol 193, Issue 3 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."

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Issue with make_average_subject
by imurrieta＠hsctmexico.com 02 Mar '20

02 Mar '20

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recon-all-failure with file links
by Ian 02 Mar '20

02 Mar '20

External Email - Use Caution Oops, looks like the files didn't attach. Here are links to the logs: https://obd-public.s3.eu-west-2.amazonaws.com/recon-all-standard_out_log.log https://obd-public.s3.eu-west-2.amazonaws.com/recon-all-status.log https://obd-public.s3.eu-west-2.amazonaws.com/recon-all.log Hi all. I have a T1 scan which I run through recon-all with: recon-all -all -parallel -subjid freesurfer (after mksubjdirs etc) On my office machine, recon-all completes successfully. On a cloud machine (16GB of ram), it fails after about 4 hours. I have attached the logs - the only immediate error I can see is "Cannot find rh.white.H". Any advice would be much appreciated, thank you. Ian -- *Ian Hardingham* Chief Technology Officer signature_873986710 ian.hardingham(a)oxfordbraindiagnostics.com <mailto:terry.pollard@oxfordbraindiagnostics.com> +44 (0)7789 770555 Oxford Centre for Innovation | New Road | Oxford | OX1 1BY Oxford Brain Diagnostics Ltd is a company registered in England and Wales | Company No. 11703979 | VAT No. 321 3026 62

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DPABI V4.3, DPABISurf V1.3 and DPARSF V5.0 were released!
by YAN Chao-Gan 02 Mar '20

02 Mar '20

External Email - Use Caution Dear colleagues, We are pleased to announce the release of DPABI V4.3, DPABISurf V1.3 and DPARSF V5.0. New features of DPABI_V4.3_200301 (download at http://rfmri.org/dpabi, please also update the docker file by: docker pull cgyan/dpabi): 1. Stability Analysis module was added. You can calculate volume-based and surface-based stability from DPABI->Dynamic & Stability Analyses. You can read our recent work for the details of stability measure: Li, L., Lu, B., Yan, C.G. (2019). Stability of dynamic functional architecture differs between brain networks and states. Neuroimage, 116230, doi:10.1016/j.neuroimage.2019.116230. 2. Field map correction was added, both for DPARSF and DPABISurf. If you want to perform field map Correction, you need to arrange each subject's field map DICOM files in one directory, and then put them in "FieldMap" directory under the working directory. i.e.:';... '{Working Directory}\FieldMap\PhaseDiffRaw\Subject001\xxxxx001.dcm';... '{Working Directory}\FieldMap\PhaseDiffRaw\Subject001\xxxxx002.dcm';... '...';... '{Working Directory}\FieldMap\PhaseDiffRaw\Subject002\xxxxx001.dcm';... '{Working Directory}\FieldMap\PhaseDiffRaw\Subject002\xxxxx002.dcm';... '...';... '{Working Directory}\FieldMap\Magnitude1Raw\Subject001\xxxxx001.dcm';... '{Working Directory}\FieldMap\Magnitude1Raw\Subject001\xxxxx002.dcm';... '...';... '{Working Directory}\FieldMap\Magnitude1Raw\Subject002\xxxxx001.dcm';... '{Working Directory}\FieldMap\Magnitude1Raw\Subject002\xxxxx002.dcm';... '...';... '...';... Then you can click the button of “FieldMap” button to set field map correction parameters. In most cases, you can use the default “0” value to let the program read the parameters (e.g., echo times) from the DICOM files. 3. Check data organization function added. For the new users of DPARSF and DPABISurf, most of the errors were caused by data organization! Please use DPABI->Utilities->Check Data Organization to check your data organization before running DPARSF or DPABISurf. This program will lead you to organize your data correctly with prompting messages! 4. Slice timing information read from DICOM files. If you are starting with DICOM files, you no longer need to set the slice timing correction parameters. Just leave it as default (slice number: 0), then DPARSF or DPABISurf will read the parameters from DICOM files. This new feature thanks to Dr. Chris Rorden's new dcm2niiX program (version v1.0.20190902). 5. DPARSF V5.0 now is compatible with BIDS format. You can start with BIDS format data by checking checkbox “BIDS to DPARSF” and setting “Starting Directory Name” to “BIDS”. 6. DPABISurf V1.3. Check and re-run fmriprep failed subjects. If for any reason, the program failed fmriprep running in DPABISurf, you just need to re-run starting with the step “Preprocessing with fmriprep” and set the “Starting Directory Name” to “BIDS” in DPABISurf_Pipeline. Alternatively, you can run a single checking step from DPABI->DPABISurf->Utilities->Re-Run fmriprep Failed Subjects. 7. DPABI->Utilities->DICOM Sorter. Now DICOM Sorter will remove illegal characters for file names in DICOM sorter. E.g., a subject id of “Wang’#$#’s” will no longer cause a problem in sorting DICOM files. 8. y_Call_DPABISurf_VIEW_FromVolume.m and y_Call_DPABISurf_VIEW.m were added. Now you can use script to call DPABISurf_VIEW to generate surface maps (with higher quality now) in batch. Remember to add “close all” in the for loop to prevent too many windows. Tips: 1) For Linux or Mac OS, please start matlab from terminal in order to reach docker in DPABI (e.g., Linux: matlab; Mac: open /Applications/MATLAB_R2018a.app/). 2) Before running DPABISurf_Pipeline, you can test the docker environment by running DPABI->DPABISurf->Utilities->Volume-Surface Projector. If the file can be successfully projected to surface, then the software is all set. Best, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Director, International Big-Data Center for Depression Research Deputy Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://rfmri.org/DPARSF>DPABI <http://rfmri.org/DPABI> <http://rfmri.org/DPARSF>, <http://dpabi.org>DPARSF <http://rfmri.org/DPARSF>, PRN <http://rfmri.org/PRN> and The R-fMRI Network <http://rfmri.org> (RFMRI.ORG <http://rfmri.org/>) http://rfmri.org/yan http://scholar.google.com/citations?user=lJQ9B58AAAAJ

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PhD Position in Multilingualism/Psycholinguistics
by Narly Golestani 01 Mar '20

01 Mar '20

External Email - Use Caution With the launch of a new ‘NCCR Evolving Language’ (http://www.snf.ch/SiteCollectionDocuments/nfs/Faktenblatt_NCCR_evolvinglang…) which involves nearly 40 different research groups from a large variety of disciplines across Switzerland, we seek to fill a PhD position for a four-year project starting in May 2020, or at the selected candidate’s convenience. Our goal is to make progress in understanding language giftedness from cognitive, psychological and neural perspectives. To this end, we plan to carry out a set of studies involving both behavioral measures of cognitive and language-related abilities (e.g. auditory/perceptual abilities, phonemic perception and production, inductive learning, working memory etc) and brain imaging measures (fMRI and sMRI). The research group involves two PIs (Golestani, Geneva; and Berthele, Fribourg) and a postdoc. Data will be collected with Francophone (mono- and multilingual) subjects. Applicants should hold an MA degree in psychology, linguistics or a related field (e.g. psycholinguistics, applied linguistics, multillingualism), have a good command French and English and have strong quantitative research and statistics skills. Additional mastery of German and experience with neuroimaging techniques would be a strong advantage. The NCCR places great emphasis on gender diversity and we particularly encourage women to apply. Applicants may send a pdf file including a cover letter, a CV, names and contact information of 2-3 references as well as any other relevant documents to Narly.Golestani(a)unige.ch<mailto:Narly.Golestani@unige.ch> and Raphael.berthele(a)unifr.ch<mailto:Raphael.berthele@unifr.ch>. Deadline for application: March 31 2020 ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Brain and Language Lab Prof. Narly GOLESTANI Department of Psychology Campus Biotech 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>http://www.brainandlanguagelab.org https://twitter.com/brain_lang_lab ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

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Postdoc position available - computational modeling and real-time fMRI neurofeedback of language
by Narly Golestani 01 Mar '20

01 Mar '20

External Email - Use Caution With the launch of a new ‘NCCR Evolving Language’ (http://www.snf.ch/SiteCollectionDocuments/nfs/Faktenblatt_NCCR_evolvinglang…) which involves nearly 40 different research groups from a large variety of disciplines across Switzerland, we seek to fill a Postdoc position for a four-year project starting in May 2020, or at the selected candidate’s earliest convenience. Our goal is to make progress in understanding the importance of prosody in language processing. To this end, we plan to carry out a set of studies involving both computational modeling of fMRI data and real-time fMRI neurofeedback to understand the mechanisms whereby prosody and rhythm support linguistic processing per se. The computational modeling work will be an extension of our recent work on the neural encoding of acoustic information in speech sounds (https://www.ncbi.nlm.nih.gov/pubmed/31285622) The research will be done in the group of Narly Golestani (www.brainandlanguagelab.org<http://www.brainandlanguagelab.org>) in Geneva, in collaboration with researchers in Switzerland and abroad (Elia Formisano in Maastricht, and Frank Scharnowski in Vienna). Applicants should hold a degree in Biomedical Engineering, Computational Neuroscience, or a related field, and should have solid experience in human brain imaging, and ideally also in computational modelling (i.e. encoding / decoding) of fMRI data, real-time fMRI based neurofeedback, machine learning, statistics and programming. The NCCR places great emphasis on gender diversity and we particularly encourage women to apply. To apply, please send a cover letter, CV, names and contact information of 2-3 references as well as any other relevant documents to Narly.Golestani(a)unige.ch<mailto:Narly.Golestani@unige.ch>. Feel free to contact me should you have any questions. Deadline for application: March 15th 2020 ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Brain and Language Lab Prof. Narly GOLESTANI Department of Psychology Campus Biotech 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>http://www.brainandlanguagelab.org https://twitter.com/brain_lang_lab ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

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Freesurfer March 2020