Freesurfer January 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
132 discussions

Non-uniform voxel size
by Julie Ottoy 13 Jan '21

13 Jan '21

External Email - Use Caution Dear freesurfer team, I am dealing with PET scans that were acquired at different sites. They do not have uniform voxel size and dimensions. I was wondering if this would be an issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf --projfrac 0.5" and vertex-wise PET group-analyses. Should I resample to a uniform voxelsize prior to these steps or does freesurfer take care of this issue internally? Thank you for the information. Best regards Julie

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mincRead error in recon-all
by Michele Valotti 13 Jan '21

13 Jan '21

External Email - Use Caution Dear Freesurfer Team, I am trying to run recon-all on a test scan, but I am getting this error: Error opening ./tmp.mri_nu_correct.mni.6973/nu1.mnc mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.6973/nu1.mnc (logs attached) I just reinstalled minc tools due to a nu_correct error I was getting, not sure if this could be a problem. I read on the mailing list that it could be a permission error but trying the suggested solutions did not solve the problem running ls -l tmp.mri_nu_correct.mni.3787/nu1.mnc returns -rw-rw-r-- 1 michele michele 22990022 Jan 4 15:01 tmp.mri_nu_correct.mni.3787/nu1.mnc Any help is greatly appreciated Thank you Michele

2 1

Editing Recon-all on Different Computers
by Boa Sorte Silva, Narlon 13 Jan '21

13 Jan '21

External Email - Use Caution Hi FreeSurfer community, Are there any reservations for editing recon-all outputs (cross, base, or long) on a different computer from which the images were originally processed? Both computers are Mac and have the same FreeSurfer version (7.1.1). I intend to use the same computer when re-running the edited images in in recon-all pipeline, but wanted to know whether editing on a different computer would be an issue. Thank you, Best regards Nárlon Cássio Nárlon Cássio Boa Sorte Silva, PhD CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia Twitter: @BoaNarlon

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Desikan Killiany Atlas Node Coordinates
by Hua, Jessica 13 Jan '21

13 Jan '21

External Email - Use Caution Dear FreeSurfer, I would like to conduct a network based statistical analysis. One of the inputs in the NBS toolbox is to provide a list of MNI coordinates for each of the brain regions in the parcellation. Is there an established list of MNI coordinates for the Desikan-Killiany atlas? And if not, do you know how I could identify the center MNI coordinate for each of the brain regions in this atlas? Best, Jessica

3 2

Open a Pre-doc position in Spain
by Rosalia Dacosta Aguayo 13 Jan '21

13 Jan '21

External Email - Use Caution Dear FreeSurfer forum, Sorry for the cross posting. We are looking to cover a position for a* pre-doc* student working in the field of life sciences (medical doctor, biologist, psychologist) to work on a project about arteriopathies and atherosclerosis. The position is in Spain, at the IDIAP Jordi Gol Research Institute in Barcelona (Spain). Candidates, please contact: rdacostaa(a)gmail.com. Best wishes, Rosalia

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starting longitudinal pipeline after mri_robust_template
by Marisa Johanna Nordt 13 Jan '21

13 Jan '21

External Email - Use Caution Hello, I have a question regarding the longitudinal pipeline: Is it possible to start the longitudinal pipeline after a template (using mri_robust_template) has already been created in a separate step? Thank you so much, Marisa

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eTIV=0.0 on volumes where control points have been added manually
by Julia Lam 13 Jan '21

13 Jan '21

External Email - Use Caution Dear all, I received values of 0.0 on variables BrainSegVolNotVent and eTIV when running aparcstats2table on volumes where I've added control points. However, when aseg2stats was used, the variable EstimatedTotalIntraCranialVol was different from 0 on all, including the edited ones. Why is that? I've attached the logfile from one of the subjects where I used control points. I really appreciate any help you can provide. Yours sincerely Julia Lam

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Re: [Freesurfer] Ubuntu_710_clone-disk1 'developer' password
by fsbuild 12 Jan '21

12 Jan '21

External Email - Use Caution Hello Adrian, Sending the info to your email shortly. - R. On Jan 12, 2021, at 15:42, Adrian Ion - Margineanu <adrian..ionmargineanu(a)kuleuven.be> wrote:        External Email - Use Caution        Hi all,Can I please get the password for this image: Ubuntu_710_clone-disk1 ?I am stuck at the 'developer' login page ..Cheers,Adrian_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Ubuntu_710_clone-disk1 'developer' password
by Adrian Ion - Margineanu 12 Jan '21

12 Jan '21

External Email - Use Caution Hi all, Can I please get the password for this image: Ubuntu_710_clone-disk1? ? I am stuck at the 'developer' login page .. Cheers, Adrian

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Postdoc and RA positions @ UConn/UCSF brainLENS Lab
by Jieyin Feng 12 Jan '21

12 Jan '21

External Email - Use Caution Hi all, Fumiko Hoeft MD PhD, Professor of the Departments of Psychological Sciences, Mathematics, Neuroscience and Psychiatry ( https://secure-web.cisco.com/1jarcQIUIbQjv36uDq2UMAWtM3a1o32H28Un4BykAlrsFg…) and Director of the Brain Imaging Research Center (https://secure-web.cisco.com/1W4BQ4p5O8b2VkVODa9Ukl2K0jZWyfT1Gpv42RvMWqO9LD…) at UConn, and Adjunct Professor of Psychiatry and Behavioral Sciences at UCSF, is now accepting additional applications of up to two postdoctoral fellows and/or research assistants (RAs) to *begin sometime between now and the fall of 2021 at UConn (possibly at UCSF for postdocs*; https://secure-web.cisco.com/1wvOkW2Jb_7WnClFkK869jkPXXQlvYMUYHZBpASrvjJInd…) The *postdoc(s)* would ideally have strong research- and publication-records in: (1) reading, dyslexia or related fields of (developmental) cognitive neuroscience; or (2) fetal, neonatal or infant neuroimaging. The latter does not have to be in reading/dyslexia, and can be in affective neuroscience. Experience in interdisciplinary research is a plus; from theory, multimodal neuroimaging (fMRI, dMRI, TMS, MRS, EEG, etc), genetics, machine learning and network approaches (see https://secure-web.cisco.com/1hBEx0yvAY8RBzyK3W1LPLkb-Wz1W0Co4pLBYErp76Cbfi…) The *RAs* would ideally have experience in the areas above, though not required. Strong management, organizational and communication/writing skills are required. Programming skills are desired but not required. There are opportunities to write grants, and publish using many of our existing and publicly available datasets. The positions are fully funded, primarily by NIH grants though a US citizenship is not required. Interested applicants should submit a cover letter, full CV, names of 3 references, and preferred location (UConn or UCSF) to Prof. Fumiko Hoeft at brainLENS(a)uconn.edu. When you write, please use subject, “[Postdoc] FIRST & LAST NAME” of “[RA] FIRST & LAST NAME”. Thanks, Jieyin

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Freesurfer January 2021