Freesurfer

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30132 discussions

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

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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

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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

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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

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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>

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Subfield parcellation in 1.5 T and 2.6 mm Thickness
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 25 Jun '20

25 Jun '20

? Hi FS developers, We were wondering whether a MRI scan that has 2.6 mm thickness + is 1.5 T would be sufficient for a subfield analysis (amygdala, hippocampus, thalamus). Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Re: [Freesurfer] .IMA to NIFTI conversion using mri_convert
by Vinny K 25 Jun '20

25 Jun '20

External Email - Use Caution Hi, I have diffusion-weighted images (DWI) from a Siemens scanner in the .IMA format. I used the following command in an attempt to convert the DWI series from .IMA to .nii/.nii.gz format.... mri_convert -it siemens_dicom -ot nii NEURO_BRAIN.00034.IMA dwi However, I get an outputted dwi file but it's in a Binary (application/octet-stream) format. Also, the bvecs and bvals files were not outputted. Any help would be appreciated. Thanks, Vinny

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Extracting CRAS from nifti (mri_info)
by Sherin Sugathan 25 Jun '20

25 Jun '20

External Email - Use Caution Dear Freesurfer team, I am a user of freesurfer. The tool mri_info provides me useful information from nifti files. As part of my project, I am using VTK to programmatically extract information like direction matrix, size, origin etc from a nifti file. However, I am unable to extract --cras information from a nifti file. Could you please throw some light on how I can extract the CRAS values from a NIFTI file using matlab or vtk or itk ot nibabel? If the CRAS values are computed, I would like to know how they are computed. Basically, I am trying to understand how I can get the CRAS values without using mri_info tool. Thanks in advance! Regards, Sherin Sugathan

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Re: [Freesurfer] Nifti to gifti conversion
by Glasser, Matthew 25 Jun '20

25 Jun '20

External Email - Use Caution You can use Connectome Workbench’s wb_command -volume-to-surface-mapping (recommend using the -ribbon-constrained option with the white and pial surfaces). You can then use wb_command -cifti-create-dense-timeseries to merge the two hemispheres and subcortical grey matter data into a CIFTI file. If you want a pipeline that does this for you, the ciftify pipeline (https://github.com/edickie/ciftify) might be a good choice if you have already done your preprocessing, or you could use the HCP Pipelines to do all of your preprocessing. Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1(a)cardiff.ac.uk> Reply-To: Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, June 24, 2020 at 7:42 AM To: "freesurfer-bounces(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu>, Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Nifti to gifti conversion External Email - Use Caution Hi Experts, I have a set of resting state data in nifti format. I want to get these data into gifti format, so I can then convert them into cifti format and run melodic ICA. I suspect using mri_vol2surf would do the trick, but I know you need to specify which hemisphere you want the projection to take place on. However, I wondered if it was possible to do this for both hemisphere, or whether there is a command to merge the two hemisphere back together into a single gifti file after running vol2surf separately? The command I am currently running is: Mri_vol2surf –src filtered_func.nii.gz –out resting_surface.gii –srcreg partial-to-struct.lta –hemi lh –projfrac 0.5 –out_type gii Any advice would be great. Thanks, 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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] mesh spatial resolution after mris_expand
by Patricia Pais Roldan 24 Jun '20

24 Jun '20

External Email - Use Caution Dear freesurfer community, I'd like to know if there's any difference between the characteristics of a white or pial surface generated during the standard recon-all and a surface generated through mris_expand (e.g. mris_expand -thickness lh.white 0.2 lh.whitePlus02). In my results, it seems that in some areas the vertices of mris_expand-generated surfaces are more separated from each other (i.e., larger triangles or lower resolution -see original question for details-). Thank you very much. Patricia On 04.05.20 09:20, Patricia Pais wrote: Dear FreeSurfer developers, I'm generating white and pial surfaces using recon-all on an MP2RAGE to later create intermediate surfaces using mris_expand (for example: mris_expand -thickness lh.white_smooth 0.2 lh.layer02, with lh.white_smooth being a smoothed version of lh.white). It all looked fine until I decided to calculate the vertex-to-vertex distance and plotted the distribution of this parameter (something like the "spatial resolution of the mesh") for all the generated surfaces. In the histograms below, you see "distance between vertices" on the X axis and "number of samples" (pairs of vertices) on the Y axis (left/right plots: left/right hemisphere, blue=sulci vertices, red=gyri vertices). The distributions are in agreement with previously published work, but I see a small peak on the left (around 0.25 mm) in intermediate surfaces, like an accumulation of points with a certain vertex-to-vertex distance instead of a gradual decrease towards 0 (pial and white are ok). I traced back the points in these bumps and I confirmed that those vertices in intermediate surfaces correspond to vertices on the left tail of the curve in the pial and white surfaces, so I'm not very worried about it, but I'd like to know whether there's some kind of minimum distance between the vertices of the surfaces generated by mris_expand or any other reason that can explain my results. Thank you very much in advance! [cid:part1.082A4986.CF854785@fz-juelich.de] Best regards, Patricia ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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