Freesurfer May 2019

freesurfer@nmr.mgh.harvard.edu

95 participants
141 discussions

Postdotoral call, human brain microstructure with MRI, Italy
by Jovicich, Jorge 09 May '19

09 May '19

External Email - Use Caution A 2-year postdoctoral call is available at the MRI Group of the Center for Mind/Brain Sciences (CIMeC) at the University of Trento, Italy. The focus of this position will involve the development, testing and validation of MRI techniques that allow quantification of function and tissue microstructure properties. The successful candidate will be part of an international multidisciplinary team developing and applying MRI techniques to study brain structure and function supporting normal higher cognitive function as well as the study of cognitive dysfunction in various neurological and neuropsychiatric conditions (including pre-surgical planning, plasticity in deaf and blind, novel markers sensitive to the progression of neurodegenerative diseases). Facilities: The CIMeC MRI neuroimaging lab uses a Siemens Prisma 3T scanner designed for research and clinical studies. The position will allow for training opportunities in pulse sequence development, brain anatomy, and translational clinical research. The fellow is expected to be able to work independently as well as part of a multidisciplinary team with supervisory responsibilities of graduate student research. The fellow will support research MRI users, will have opportunities to develop new ideas and advance their own research interests in an international academic environment. Beyond work, there are outstanding opportunities for enjoying outdoors activities. Requirements: Minimum qualifications are a doctoral degree in cognitive neurosciences, physics, engineering, computer sciences or related area, strong scientific publication record, and demonstrated expertise in MRI methods development and applications. The ideal candidates should be proficient in programming, such as C++, Matlab. Experience in pulse sequence design, particularly on Siemens platform, and/or image reconstruction will be a plus. Additional requirements include high self-motivation, ability of solving research problems independently, and excellent communication skills. Contact: Jorge Jovicich, Ph.D, MSc, Associate Professor (jorge.jovicich(a)unitn.it) Attending ISMRM, contact me for an informal meeting if interested Postdoc call: http://bit.ly/CIMEC-MRI-Postdoc-Call-2019 -- Jorge Jovicich, Ph.D. MR Lab Head Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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Job Opening: Research Associate Haskins Laboratories
by Meaghan Perdue 08 May '19

08 May '19

External Email - Use Caution Research Associate Job Announcement, May 2019: Research Associate Haskins Laboratories, 300 George Street, Suite 900, New Haven CT 06511 Project Director: Nicole Landi Qualified individuals are invited to apply for a full-time Research Associate position at Haskins Laboratories (https://haskinslabs.org) The successful candidate will join the labs of Professors Nicole Landi, Elena Grigorenko, and Kenneth Pugh which investigate the cognitive and neural bases of reading development and disability using behavioral and neuroimaging techniques (MRI, EEG and NIRS). This position will primarily involve analysis of MRI data; successful applicants will be involved in all aspects of the research process. Requirements include: - BA or BS in Psychology, Cognitive Science, Neuroscience or related field - Experience with structural or functional MRI data processing and relevant software (e.g., AFNI, SPM, FreeSurfer, FSL) Additional relevant skills include: - Programming experience (e.g., Python, Matlab) - Experience with statistical analysis (e.g., SPSS, R) - Experience with data management software (e.g., REDCap, Qualtrics) Interested applicants should contact Tammy Ursini, <ursini@haskins.yale.edu?subject=Lab%20Manager%3A%20Dr.%20Richard%20Aslin> Office Manager (ursini(a)haskins.yale.edu) with a cover letter, resume, copy of (unofficial) transcripts, and the names of three potential references. Please note “Landi Lab”, in the subject line of your email. The position will remain open until filled, with an anticipated start date of August 1, 2019 or sooner (a later start date is possible). Compensation is commensurate with skills and experience. Haskins Laboratories is a private, non-profit research institute with a primary focus on speech, language, reading, and their biological basis. Haskins has long-standing, formal affiliations with the University of Connecticut and Yale University. Haskins Laboratories is an Equal Opportunity Employer. -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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Visualizing Volumetric Files on Surface
by Maedeh Khalilian 08 May '19

08 May '19

External Email - Use Caution 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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Re: [Freesurfer] Cortex reconstruction using MRI with contrast
by Dengyu Wang 08 May '19

08 May '19

External Email - Use Caution Hi Bruce, My previous email with the wm.mgz and orig.nofix files was held by the system because of the big size. So in this email I attached some pictures about the wm and orig.nofix visualized in Freeview: Hope to get your opinion. Thank you! Best, Dengyu > On May 8, 2019, at 11:01 AM, Dengyu Wang <wangdy1995(a)gmail.com> wrote: > > Hi Bruce, > Thank you for your remind and I will keep in mind in the future. > > Here are the wm.mgz, lh.orig.nofix and rh.orig.nofix > > <wm.mgz> > <lh.orig.nofix> > <rh.orig.nofix> > > I tried to open in Freeview but Freeview always collapsed. > > Best, > Dengyu > >> On May 8, 2019, at 10:45 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >> Hi Dengyu >> >> I meant images of the brain. In general don't send us images of text - just send us the text so we can search and paste and such. In this case you have a huge defect that is probably caused by dura connecting to the wm. You need to look at the orig.nofix surfaces and the wm.mgz. You might need to make the skull stripping more aggressive and/or manually edit out some of the dura, but I can't tell without seeing the dataset. >> >> cheers >> Bruce >> On Wed, 8 May 2019, Dengyu Wang wrote: >> >>> External Email - Use Caution >>> Hi Bruce, >>> Thank you for your reply! And here is the detail: >>> >>> I use the command below to start the reconstruction: >>> >>> >>> >>> 366 defects are found in the process: >>> >>> >>> >>> And then says 281 defects to be corrected, and starts correcting the defect: >>> >>> >>> And then it gets stuck in correcting defect 46 and can’t move on: >>> >>> >>> We won’t have problem with t1 image without contrast, but in this special case we only have t1 with contrast. Do you have any ideas about this problem? Thank you! >>> >>> Best, >>> Dengyu >>> >>> >>> >>>> On May 7, 2019, at 4:37 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >>>> Hi Dengyu >>>> you need to tell us what went wrong. We have reconned lots of brains with contrast, although sometimes the skull stripping needs to be played with to get it to work >>>> cheers >>>> Bruce >>>> On Tue, 7 May 2019, Dengyu Wang wrote: >>>> >>>>> External Email - Use Caution >>>>> Hello FreeSurfer developers, >>>>> I am writing to ask about problem I met when reconstructing cortex from MRI with contrast? I had one subject that had only with contrast MRI images, and the recon-all can’t finish successfully. Is there any method or parameter setting that can solve the problem? Thank you! >>>>> Best, >>>>> Dengyu >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Freesurfer default git clone branch
by Bignamini Christopher 08 May '19

08 May '19

External Email - Use Caution Dear list members, I would have a question about the naming of Freesurfer branches: I cloned the repository in order to build the code on my system and the default branch is the dev one. Should I switch to master in order to work with a stable code version or the dev one is fine? Thank you very much in advance for your attention. Best regards Christopher Bignamini

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Cortex reconstruction using MRI with contrast
by Dengyu Wang 08 May '19

08 May '19

External Email - Use Caution Hello FreeSurfer developers, I am writing to ask about problem I met when reconstructing cortex from MRI with contrast? I had one subject that had only with contrast MRI images, and the recon-all can’t finish successfully. Is there any method or parameter setting that can solve the problem? Thank you! Best, Dengyu

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White surface area and cortical surface area
by Ting Li 08 May '19

08 May '19

External Email - Use Caution Dear Freesurfer Experts, I have a very simple question. The white surface area we extract from the ?h.aparc.stats is the same area we used in the mri_surf2surf by parameter area? or the mri_surf2surf is the pial surface area? I am looking forward to your response. Thanks a lot! Best regards, Ting

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Running multiple variables in mri_glmfit
by Erik Lindberg 08 May '19

08 May '19

External Email - Use Caution Dear Freesurfer experts, I am in the processing of running correlation with cortical thickness for almost 500 CSF variables. Thus I would like to use some sort of script. I previously used the common steps (mri_preproc, mri_glmfit and mri_glmfit-sim) but this procedure does not allow a .fsgd file with all the 500 CSF variables in it … correct? When running qdec many csf variables can be in the file … but then I cannot run it by script … right? So I wonder if there is a way to use one large file with the CSF data and then to make a script so that each variable is run iteratively until all is finished. Best case scenario I would also like to include snapshots from each correlation analysis. Is this possible to do? Thanks Olof Lindberg

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skullstripping outside freesurfer
by Eric Cunningham 07 May '19

07 May '19

External Email - Use Caution Dear Freesurfer Experts, I have recently processed some data with the following 2 steps: 1) Perform skullstripping outside freesurfer to generate a nifti file (mostly using AFNI). 2) Run that through freesurfer using the -noskullstrip flag. Comparing the results from this with just running freesurfer alone, I found that the eTIV was significantly smaller, and not terribly well correlated (R^2 of .65). When looking at cortical volume measurements, it is generally considered a good idea to correct for eTIV. How would you recommend doing so in this case? Freesurfer version 5.3. Thanks, -Eric

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funcroi-table-sess
by Nasiriavanaki, Zahra 07 May '19

07 May '19

Dear Freesurfer experts Hi I have a question about funcroi-table-sess, and I appreciate if you could please find a time to reply. Is there anyway that funcroi-sess-table can give out the activation values in each timepoint separately? Right now I can get the average of activation in each subject (in a specific region of interest and a specific contrast) by using the below commands, and I was wondering if I can get the values in each timepoint. funcroi-config -label ${lable}.label -roi ${subj}/${label_lh}.cfg -analysis loom.lh -force funcroi-sess -roi all_subjects/${subj}/${label}.cfg -s all_subjects/$subj -d . funcroi-table-sess -roi all_subjects/${subj}/${label}.cfg -s all_subjects/$subj -d . -o all_subjects/$subj/ROI_analysis/${label_lh}_${contrast}.txt -c $contrast -m cespct Thanks MOna

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Freesurfer May 2019