Freesurfer May 2019

freesurfer@nmr.mgh.harvard.edu

95 participants
141 discussions

How to get the difference between motion, NU intensity correction images and the originate image?
by chen 11 May '19

11 May '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set. According to my results, there exsit difference between ROIs. So, i want to check the difference between the originate image and the images after motion and NU intensity correction to confirm the most variation area. How can i get this information?I am looking forward to your kind suggestions.Best regards,Jiachen ------------------

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7T submillimeter resolution processing
by Zeng,Victor (BIDMC - Psychiatry) 10 May '19

10 May '19

Hi all, I have a 7T dataset that I would like to have assistance in running FS6.0 for, and I have used this page as a reference: https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon I have some questions about the recon-all command, namely what the $IMAGE variable actually means. Also I have the $EXPERT_FILE as a txt file that just says: mris_inflate -n 100?. That is fine as well, right? Also I would like to know if the hippocampal/amyg nuc subfield parcellations is designed for 7T usage (In our neuroimaging lab, we've been using it for both 1.5T and 3T). Thanks for your help. 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] A Question about How to Map Parcels of the Cortex on the surface of the Brain Cortex
by Bruce Fischl 10 May '19

10 May '19

Hi Mahsid matlab is probably the easiest way, but without knowing what format you have them in it isn't easy for us to say. In matlab you can use write_annotation or write_ascii_curv or something to get it into a format we can handle cheers Bruce cheers Bruce On Fri, 10 May 2019, mahshid fouladivand wrote: > > External Email - Use Caution > > Hello Dear Freesurfer Experts, > > I have a high resolution brain cortex parcellation that is not extracted from Freesurfer. Now I > want to display the nodes(each parcels) on the pial and inflated surfaces. Both pial and inflated > surfaces have been extracted from T1mprage image of the corresponding subject using recon-all. > Also, the parcels and the T1 image are in the same space. Now, I am wondering is it possible to map > these parcels on the Freesurfer pial/inflated surface? > By the way, How can I create an .annot file for my parcels? > If you could help me with this, I really appreciate your help. > > Regards, > Mahshid > >

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apply m3z warp to list of coordinates
by Benjamin Wittevrongel 10 May '19

10 May '19

External Email - Use Caution Dear, As part of our invasive work, we would like to extract the mni coordinates of intracranial electrodes. To this end, we follow the following procedure: 1) Pre-implant MRI and Post-implant CT are coregistered using SPM. 2) The pre-implant MRI is processed using the recon-all function. 3) The CT is conformed to the 256^3 space, using 'mri_convert ct.nii ctConformed.nii --conform --nochange' 4) The coordinates (in mri-space, i.e. row-column-slice) of the intracranial electrodes are extracted using a custom semi-automated Matlab script. 5) When recon-all finished, the subject is being warped to MNI space, using 'mri_cvs_register --mov subjectId --mni' The last step returns the non-linear warp in an m3z-file. I now want to apply this transformation to the coordinates of the electrodes. For this, I load the m3z-file in matlab, using the 'mris_read_m3z.m' provided by the freesurfer development repository, which gives me two 4-dimensional matrices (256 x 256 x 256 x 3): vol-orig and vol-dest. However, I cannot find any documentation how to interpret these matrices. Could you provide any information on how I would interpret these matrices, and how to apply the warp to the list of CT coordinates (in row-column-slice) to obtain their mni coordinates? Thank you in advance. Best regards, Benjamin Wittevrongel Laboratory for Neuro- and Psychophysiology KU Leuven

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Primary slice direction and image origin?
by falk.luesebrink＠med.ovgu.de 10 May '19

10 May '19

External Email - Use Caution Dear all, This is not directly related to FreeSurfer, however, can anyone tell me how the primary slice direction and image origin is determined from the DICOM header as displayed for example using mri_info? Best, Falk ............................................... [klinikum_logo_schmal_e-mail_blau] Universitätsklinik für Neurologie Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg Telefon: +49-391-6117-512 falk.luesebrink(a)med.ovgu.de<mailto:falk.luesebrink@med.ovgu.de> http://www.kneu.ovgu.de/kneu.html

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aparc.pial.stats
by Ting Li 09 May '19

09 May '19

External Email - Use Caution Dear Freesurfer Expert, Is there a way to get the aparc.pial.stats in one command like aparcstats2table? Thanks a lot! Best regards, Ting

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Fwd: Visualizing Volumetric Files on Surface
by Maedeh Khalilian 09 May '19

09 May '19

External Email - Use Caution > From: "Maedeh Khalilian" <M.Khalilian(a)sutech.ac.ir> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Date: Thu, 09 May 2019 01:24:58 +0430 > Subject: Visualizing Volumetric Files on Surface > Dear FreeSurfer experts; > I have created some volumetric(.nii) files in FreeSurfer (the procedure > is > as following: lh/rh.aparc.annot> mri_divide_parcellation > > mri_aparc2aseg > > deleting subcortical and white matter regions in order to keep just > cortical > regions on GM). > > Now I wanna visualize my volumetric files on surface so that I myself > can > determine the color of each region. But I dunno how to do it exactly. > I would be grateful if u could help me with that. > Thanks in advance > Best regards > Maedeh, > >

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PostDoc position in Population Neuroimaging available, Connectivity Group, Research Centre Jülich (Germany)
by Svenja Caspers 09 May '19

09 May '19

External Email - Use Caution The Connectivity Group (lead: Prof. Dr. Svenja Caspers) of the Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich (Germany) is seeking applications for a *PostDoctoral Research Position in Population Neuroimaging* ** (E 13 TVöD; 39 hours/week) The Connectivity Group focuses on the investigation of brain variability throughout the life span in relation to environmental and genetic factors, with a particular focus on the aging brain and taking advantage of large population-based cohorts who underwent MR neuroimaging (e.g. UK Biobank, German National Cohort, Human Connectome Project, 1000BRAINS). Specific aspects include structural, resting-state functional connectivity as well as advanced diffusion imaging for structural connectivity analyses, including graph-theory analyses. Large cohorts of thousands of subjects are processed using adjusted pipelines and workflows for high-throughput imaging analytics based on common software packages (e.g. FreeSurfer, FSL, MRtrix) on available high-performance computing systems of the Research Centre Jülich. Current interests cover topics in advanced statistical analyses and data-driven methods using machine-learning and deep learning approaches. These efforts are part of current projects within the Human Brain Project (HBP). The successful candidate has a PhD in neuroscience, computer science, psychology, medicine or related fields and has experience with processing and analyses of MR neuroimaging data in larger cohorts. A strong interest and expertise in applying machine-learning to large neuroimaging datasets is highly desired to enable the candidate to conduct novel and innovative research projects to understand the normal variability of brain aging. Your profile: - deep knowledge of several software packages for processing of neuroimage data (e.g. FreeSurfer, FSL, MRtrix), also including respective python packages (e.g. NiPy, DiPy) and longitudinal pipelines - profound expertise in multivariate statistical analyses, including usage of software for large-scale statistical analyses (e.g. R) and modelling of non-linear and longitudinal effects - profound programming skills (e.g. Python) enabling high-throughput big data analyses - knowledge of and interest in machine-learning and deep-learning techniques to be applied to large neuroimage datasets of population-based cohorts - familiarity in working with large datasets - strong publication track record - ability to work independently - high proficiency in English The applicant will become part of an interdisciplinary team of PostDocs, PhD and MD students with various backgrounds. He / she will have ample possibilities to expand his / her own knowledge and expertise and interact and collaborate with colleagues from different fields, including big data analytics, genetics, epidemiology and microscopic analyses. With our group closely collaborating with the Jülich Supercomputing Center, the applicant will join current efforts in bringing population neuroimaging analytics to high-performance computing clusters for efficient and novel analyses approaches. The applicant will be involved in the supervision and mentoring of PhD, MD, master and bachelor students. Funding for the position is available for two years. Applications will continue to be received until the position is filled. Please send your comprehensive application, including CV, publication record, copies of relevant certificates and either reference letters or names of two potential references to Prof. Dr. Svenja Caspers (s.caspers(a)fz-juelich.de <mailto:s.caspers@fz-juelich.de>). -- ============================== *Univ.-Prof. Dr. med. Dr. rer. pol. Svenja Caspers * Direktorin Institut für Anatomie I Heinrich-Heine-Universität Düsseldorf 40221 Düsseldorf (Deutschland) Tel.: 0211-8112678 Email: svenja.caspers(a)hhu.de svenja.caspers(a)med.uni-duesseldorf.de /und / Arbeitsgruppe Konnektivität Institut für Neurowissenschaften und Medizin (INM-1) Forschungszentrum Jülich GmbH 52425 Jülich (Deutschland) Tel.: 02461-611742 Email: s.caspers(a)fz-juelich.de

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Questions about registration
by Yang, Weiqi 09 May '19

09 May '19

Hi, I am new to Free Surfer and am working on the resting state fMRI data analysis using FS-FAST. When I used the tkregister-sess command to see the registration quality (from structural image to fMRI image), I found that there is one registration not good (QA value = 0.9). So I did manual registration and save the reg. However, I don't know how to use my manual registration file as input for the bbregistration. My solution is that I overwrote the original registration file and ran the automatic registration again. Is there any neater way to do this? How to check the QA value for the updated registration? And I also found there are registration files in both fsd directory (ex. BOLD ) and the session directory (ex. 001). Are these registration files the same? Thank you in advance for your time. Best, Weiqi

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I: help segmentation
by Erika Portera 09 May '19

09 May '19

External Email - Use Caution ________________________________ Da: Erika Portera Inviato: giovedì 9 maggio 2019 09:08 A: freesurfer-request(a)nmr.mgh.harvard.edu Oggetto: help segmentation Good morning, I need your advice for a segmentation problem that I can't solve: I have noticed that FS does not recognize extracortical lesions (between gray and white) and tends to exclude them. I tried to include them with control points and adding voxel of white substance, following the tutorial, but the problem is not solved. Could you advise me? Thank you[cid:031365d1-0794-4660-a6d1-fdd3f6a9ad5f]

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Freesurfer May 2019