Freesurfer June 2020

freesurfer@nmr.mgh.harvard.edu

91 participants
130 discussions

Position open: Research Engineer in Neuroimaging at BBRC - Barcelona
by Juan Domingo Gispert López 29 Jun '20

29 Jun '20

External Email - Use Caution The Alzheimer's Prevention Program of the Barcelonabeta Brain Research center is seeking a Research Engineer in Neuroimaging. For further information on the position, please visit the following link: https://fpmaragall.org/wp-content/uploads/2020/06/Research-Engineer-in-Neur… To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV 3) The names of up to three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: rh(a)barcelonabeta.org Subject: Research Engineer in Neuroimaging Deadline: 10th of July -- *Juan Domingo Gispert*Group Leader - Neuroimaging *BarcelonaBeta* * Brain Research Center (BBRC) *jdgispert(a)barcelonabeta.org T. (+34) 93 326 31 67 C/ Wellington, 30 <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> 08005 Barcelona <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> www.barcelonabeta.org www.fpmaragall.org ------------------------------ Confidencialitat correu electrònic BBRC <https://www.barcelonabeta.org/ca/politica-privacitat-web>. Confidencialidad correo electrónico BBRC <https://www.barcelonabeta.org/es/politica-privacidad-web>. E-mail confidentiality BBRC <https://www.barcelonabeta.org/en/privacy-policy-web>. Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving paper.

1 0

mri_vol2surf for NIFTI to GIFTI conversion
by Mason Wells 29 Jun '20

29 Jun '20

External Email - Use Caution Dear experts, I posted a message last week about converting NIFTI files into GIFTI format, then GIFTI to CIFTI, whilst keeping these functional data in the same space as the subjects FS surface. I got some information RE usign the HCP workbench, but I wondered if running mri_vol2surf could achieve the same thing as running the wb_command? For example, is it advisable to run the following command for each hemisphere and then merge them into a single GIFTI/CIFTI in the next steps? * mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii --srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii I have also tried the wb_command option but this has been unsuccesful: I first ran the mris_convert to convert the relevant surf files into .gii format (from FS format) * e.g. mris_convert lh.pial lh.pial.surf.gii I then applied the transformation to align the filtered_func to the T1 * mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta --fstarg --o movie_t1_space.nii.gz I then tried to run the following wb command * wb_command -volume-to-surface-mapping /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii Which resulted in this subsequent error. ERROR: NAME OF FILE: movie_t1_space.nii.gz PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat Unable to allocate memory for reading the file. File Size: 3.24 Gigabytes Note: The amount of memory required to read a data file may be substantially larger than the size of the file due to the way the file's data is organized in memory or compression of data within the file. Any advice on how to convert NIFTI to GIFTI and then GIFTI to CIFTI whilst keeping the data in the subjects space would be really appreciated. Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

1 0

Visualizing Talairach Registeration
by Wakim, Kathryn-Mary 29 Jun '20

29 Jun '20

External Email - Use Caution Hi all, I’m a new FreeSurfer user, so I’d like to thank you all in advance for your patience! After running recon-all to completion, I reviewed the log file and found the warning "#@# Talairach Failure Detection.” I am assuming that this is a warning and not a hard failure, because it seems that recon-all has run to completion “without error” (according to the log file). I attempted to follow these instructions to verify my Tal registstration output: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview#:~:…)<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview#:~:…)> However, it seems based on archived Freesufer forum posts that the GUI for tkregister2 is no longer compatible with the current Mac OS, and I was therefore unable to use this tool. I’m wondering if someone can provide me with some alternate instructions for how to view the output of the Tal registration so that I can verify whether or not there has been a registration error. Warm regards, Kamy Wakim

2 2

Trouble With Pial Surface Reconstruction Using FLAIR Image
by Pankush Kumar 29 Jun '20

29 Jun '20

External Email - Use Caution Hello, I was wondering if I can get some help. Every time I try to run my T1 image with a T2 FLAIR to enhance pial surfaces, I get the following message: Computing pial target locations using multimodal (2) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300 inside_peak_pct = 0.01, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=2 Creating lowres distance volumes t=0.000581909 Creating white distance volumes t=0.773706 (box.dx, box.dy, box.dz) = (118, 218, 310) (region->dx, region->dy, region->dz) = (118, 218, 310) (region->dx, region->dy, region->dz) = (118, 218, 310) Creating pial distance volumes t=1.42513 (box.dx, box.dy, box.dz) = (124, 226, 314) (region->dx, region->dy, region->dz) = (124, 226, 314) (region->dx, region->dy, region->dz) = (124, 226, 314) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 2.14683 Starting loop over 106284 vertices vno = 0, t = 2.14683 error: Cannot allocate memory error: HISTOalloc(-2147483648): could not allocate histogram I am currently using the command recon-all -subject <subject name> -FLAIR 106_T2w_FLAIR_AX_SENSEBrain_res.nii.gz -FLAIRpial -all -noskullstrip The error log is attached below. I looked at filled.mgz, it does not seem to have any skull or cerebellum in it. Any help would be appreciated! Sincerely, Pankush Kumar

4 10

Error in qdec
by Mateus Aranha 29 Jun '20

29 Jun '20

External Email - Use Caution Hello, Iḿ trying to perform a group analysis using qdec, but the analysis stops at 70% and the following error message is shown: [image: Screenshot from 2020-06-29 13-03-27.png] How should I proceed? Thanks, Mateus

2 1

Precise MNI152 space
by Inês Pereira 29 Jun '20

29 Jun '20

External Email - Use Caution Dear FreeSurfer developers, Which MNI152 space is used within FreeSurfer? Is it the MNI152 nonlinear 6-th generation (as in, for example, FSL), or another one, like MNI152 nonlinear 2009a, 2009b or 2009c? I wasn’t able to find this information in the fswiki. I checked https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems and the documentation of certain functions, such as mri_cvs_register. Thank you for your help! All the best, Inês Pereira

2 1

error in "recon-all -all -s subject -hippocampal-subfields-T1": exited with errors
by Shimura, Yuki 29 Jun '20

29 Jun '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute calculate hippocampal volumes, as described on the MultiModal FMRI tutorial "Segmentation of hippocampal subfields"(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) but I get the following error when I run the following command: Command: recon-all -s subject -hippocampal-subfields-T1 Error: recon-all -s TNU_AIDAZ_3002_T1 exited with ERRORS at Mon Jun 22 15:42:08 JST 2020 (TNU_AIDAZ_3002_T1 is the subject name) Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. Here are few contexts: a) I had the following command for recon-all for my subject: recon-all -i ${SUBJECTS_DIR}/subject_structual_image_file.nii -s subject -all -qcache -3T b) this was done without an error c) now I want to do " recon-all -s subject -hippocampal-subfields-T1" 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: CentOS release 6.7 (Final) 3) recon-all.log: see attached

2 2

Scientific Project Coordinator for an open science, large-scale collaboration
by Caspar M. Schwiedrzik 28 Jun '20

28 Jun '20

External Email - Use Caution Dear all, If you are seeking a challenge, if you are dynamic and enthusiastic about managing a large consortium of scientists, then do not hesitate to apply for the *Scientific Project Coordinator *position in my group at the Max Planck Institute for Empirical Aesthetics. You will be coordinating this <https://science.sciencemag.org/content/366/6463/293> project which was recently features in science, and involves 11 institutions across Europe, the US and China running an adversarial collaboration project aimed at understanding the neural foundations of consciousness. This is a unique opportunity to contribute to the development of an open science model for large-scale collaborations. We are looking for an internationally experienced scientist with knowledge of science management, networking, and international collaboration, and a keen interest in developing practices and procedures for open science. This is a full-time position for 2 years. More information on the job requirements and the position can be found here <https://www.aesthetics.mpg.de/karriere/jobs/scientific-project-coordinator-…> . For enquiries concerning this job opportunity please contact *Dr. Lucia Melloni: **lucia.melloni(a)ae.mpg.de <lucia.melloni(a)ae.mpg.de>**.* Please submit your application - preferably online in a single pdf - including a CV and a cover letter describing your background, experience and motivation as well as the names of two references, who have previously agreed to be contacted, *no later than July 31, 2020 *to: *job(a)ae.mpg.de* <job(a)ae.mpg.de> Looking forward to the applications! Best wishes, Lucia Melloni

1 0

Brodmann area labels
by Peng Liu 26 Jun '20

26 Jun '20

External Email - Use Caution Dear Freesurfer experts, I was trying to perform some ROI analysis with results obtained from recon-all. However I noticed that after recon-all, the labels created were like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to create are like 'lh.BA3b.label'. I have tried mri_annotation2label command, but the results I got were not as wanted either. Does anyone know how to create labels like 'lh.BA3b.label'? Any help would be appreciated a lot! Many Thanks PL -------------------------------------------- [image: Otto-von-Guericke University Magdeburg] Peng Liu, PhD Candidate Institut für Kognitive Neurologie und Demenzforschung (IKND) Otto-von-Guericke Universität Magdeburg Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Leipziger Str. 44| Haus 64| Raum 217 39120 Magdeburg, Deutschland Email: peng.liu@med.ovgu.de/Peng.Liu@dzne.de Phone: +49 391 67 25074

4 9

Postdoc in fMRI/Computational Neuroscience
by Michael Marxen 26 Jun '20

26 Jun '20

External Email - Use Caution Dear colleagues, we are currently looking for a Postdoc for the analysis of fMRI and behavioural data in the context of the Collaborative Research Centers CRC 940<http://www.sfb940.de/> 'Volition and Cognitive Control: Mechanisms, Modulators, and Dysfunctions', and the newly established TRR 265<https://sfb-trr265.charite.de/en/> 'Losing and Regaining Control over Drug Intake: From Trajectories to Mechanisms to Interventions'. More details can be found in the attachment. For further information, please, contact Michael.smolka(a)tu-dresden.de<mailto:Michael.smolka@tu-dresden.de>

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer June 2020