Freesurfer August 2019

freesurfer@nmr.mgh.harvard.edu

100 participants
144 discussions

binary version of brainmask?
by Chris Adamson 26 Aug '19

26 Aug '19

External Email - Use Caution Freesurfer, Is it possible to get mri_watershed to produce a binary mask version of brainmask.mgz/brainmask.auto.mgz? Thank you, Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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Invalid License Key Error for Freesurfer 5.1
by An Lijun 26 Aug '19

26 Aug '19

External Email - Use Caution Hello Freesurfer developers, Right now I am trying to use Freesurfer 5.1.0. But the software showed ERROR “Invalid FreeSurfer license key found in license file”. We tried to apply license online, however, the license provided online is now for 6.0.0 version and it seems not applicable for 5.1.0 since I still got the same error message as before. May I ask how to get the licnese of 5.1.0? Thanks for your help! ----------------------------------------------------------------------------------------------------------------------------------- Best Regards, An Lijun

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trouble with freeview View > Show Color Scale
by Elizabeth Olson 26 Aug '19

26 Aug '19

External Email - Use Caution Hello, I'm having a bit of trouble with the Show Color Scale option. I have run TRACULA and have loaded a text file containing p-values from an analysis (Spline Color: Heatscale, Scalar map: my p-values file). The values display correctly on the tract. However, when I use View > Show Color Scale, it looks like the color scale is generated is for the black-and-white volume, instead of for those values. See attached screenshot. I'm instead trying to generate a Color Scale at the right of the figure that shows which colors (yellow to red) correspond to which p-values. Thanks for your help, Liz

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Re: [Freesurfer] mri_vol2surf fails
by Greve, Douglas N.,Ph.D. 26 Aug '19

26 Aug '19

Are those values actually 0 or just very small? Is that area dark on the T2*? On 8/26/19 11:20 AM, Sackl, Maximilian wrote: > External Email - Use Caution > > Thank you for the prompt answer! > > No, the T2* map within the pial and WM does include values ... > Any ideas? > > On 26.08.2019 16:59, Greve, Douglas N.,Ph.D. wrote: >> You should bring up the T2* with the surfaces. Is it possible that the >> T2* just did not include that particular bit? >> >> On 8/26/19 10:38 AM, Sackl, Maximilian wrote: >>> External Email - Use Caution >>> >>> Dear FreeSurfer experts, >>> >>> I was trying to perform a GLM fit with T2* data, projected on the >>> cortical surface. >>> >>> For the preparation of the 4D-input file (needed for mri_preproc) I used >>> the mri_vol2surf command and encountered the following problem. There >>> appear regions without any values, (screenshot mri_vol2surf_output.png), >>> although the segmentation of the pial and WM surface seem to be correct. >>> (screenshot pialSurface.png). >>> >>> Do you have any idea, how to solve this problem? >>> >>> >>> Thank you very much! >>> >>> Best regards, >>> Maximilian >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Question re: hippocampal & amygdala subdivision files.
by Jamie Hanson 26 Aug '19

26 Aug '19

External Email - Use Caution Dear Freesurfer List, I had a (hopefully) quick question re: output files from the hippocampal and amygdala subdivision routines. I know that there are multiple parcel schemes for the hippocampus (HBT, FS60, and CA), and per this thread ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57898.html) the final subfield segments are "computed from none of those volumes, but the parent of all of them". I wondered however if there was an MGZ file that corresponded to the final/combined sub-divisions? Or if there was a way to output this? My group was interested in doing some spatial and surface analyses of sub-divisions (using Spherical Harmonics or some other related techniques). And I understand what the different MGZ files were in the mri directory (e.g., CA.FSvoxelSpace.mgz, FS60.FSvoxelSpace.mgz, HBT.FSvoxelSpace.mgz), but what was the file without any suffix (e.g., lh.hippoAmygLabels-T1.long.v21.mgz)? Or is that the file I'm looking for? Any information is deeply appreciated! Thanks much, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org

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mri_vol2surf fails
by Sackl, Maximilian 26 Aug '19

26 Aug '19

External Email - Use Caution Dear FreeSurfer experts, I was trying to perform a GLM fit with T2* data, projected on the cortical surface. For the preparation of the 4D-input file (needed for mri_preproc) I used the mri_vol2surf command and encountered the following problem. There appear regions without any values, (screenshot mri_vol2surf_output.png), although the segmentation of the pial and WM surface seem to be correct. (screenshot pialSurface.png). Do you have any idea, how to solve this problem? Thank you very much! Best regards, Maximilian -- Maximilian Sackl, BSc Department of Neurology Medical University of Graz Auenbruggerplatz 22, A-8036 Graz maximilian.sackl(a)medunigraz.at www.neuroimaging.at Tel +43/316/385-13691

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Job ad: Small animal MRI faculty position at U. of Delaware
by Timothy Vickery 26 Aug '19

26 Aug '19

External Email - Use Caution Assistant/Associate Professor, Behavioral Neuroscience University of Delaware: College of Arts & Sciences: Psychological & Brain Sciences Location: Newark, DE The Department of Psychological and Brain Sciences ( https://www.psych.udel.edu) at the University of Delaware invites applications for an Assistant or Associate Professor in Behavioral Neuroscience to begin September 1, 2020. We seek to hire a research scholar with a neuroscience background in small animal brain magnet resonance (MR) imaging within any area of research. Scholarly excellence is preferred above all else. Ideal candidates will have extensive experience in neuroscience-oriented MR research and demonstrate innovative scholarship, with research that complements or adds to existing faculty expertise. This is an outstanding opportunity for a scholar to join and strengthen the growing Department of Psychological and Brain Sciences and its research and teaching missions. The Behavioral Neuroscience area has faculty focusing on spatial memory, fetal alcohol spectrum disorders, developmental psychobiology, social information processing, behavioral epigenetics, developmental neuroimmunology and endocrinology, neurobiology of emotional behavior, and stress-related hormonal and arousal systems in PTSD. Other faculty members in the Clinical, Cognitive, and Social Psychology areas in the Department have several active research programs utilizing our human MRI scanner. There are also many collaborative and synergistic possibilities with existing researchers throughout University of Delaware’s colleges. The candidate should enjoy interacting and collaborating with a diversity of researchers and students from various disciplines. An innovative leader in research and teaching, the University of Delaware combines a rich historic legacy with a commitment to education and the latest in advanced technology. With external funding exceeding $200 million per year, the University ranks among the top 100 universities in federal R&D support for science and engineering. Enhanced by state-of-the-art facilities, research is conducted across all seven colleges and numerous interdisciplinary institutes and centers. Relevant staffed facilities on campus include the new 11,600 square foot Center for Biomedical and Brain Imaging (http://cbbi.udel.edu) housing a new 9.4T/20cm Bruker MRI for small animals and a 3T Siemens Magnetom Prisma for humans; an animal housing and research facility attached to the CBBI; a 103,000 square foot Health Sciences Complex; a 194,000 square foot Interdisciplinary Science and Engineering Laboratory; and the Delaware Technology Park, where entrepreneurial and academic research labs are co-located. The NIH-supported Delaware Center for Neuroscience Research in collaboration with Delaware State University, and the Delaware Health Sciences Alliance (DHSA), a partnership among the University of Delaware, Christiana Care Health System, Nemours/Alfred I. du Pont Hospital for Children, and Thomas Jefferson University, provide infrastructure and opportunity for innovative basic, clinical and translational collaborations. The University of Delaware is located in Newark, Delaware, which is only a short drive or train commute from Philadelphia, PA. UD is also within driving distance of New York City, Baltimore, Washington DC, the Poconos and some of the finest beaches in the country, making it an ideal location for day or weekend trips. QUALIFICATIONS Applicants for this position must have earned a Ph.D., have a history of high-level publications in behavioral neuroscience or related fields, and conduct fundable research. APPLICATION INSTRUCTIONS To apply, please visit the submission website at https://careers.udel.edu/cw/en-us/listing/ and search for job # 494146 Applicants should submit a cover letter, a statement of research, a current curriculum vitae, three representative publications, and contact information for three confidential letters of reference. Inquiries, but not application materials, should be emailed to Jeffrey Rosen, Chair of the Behavioral Neuroscience Faculty Search committee, jrosen(a)udel.edu. Review of applications will begin on October 1, 2019 and will continue until the position is filled. The Department of Psychological and Brain Sciences holds diversity, equity, and inclusion as important values. We view diversity broadly, including but not limited to an individual's race, age, ethnicity, gender identity, sexual orientation, socioeconomic status, disability status, beliefs, and culture, as well as how those identities intersect. Supporting diversity in our faculty, student body, and staff, as well as valuing and respecting diversity in our teaching, research, service, and clinical work, represent important priorities that contribute to the strength of the department. We encourage the open exchange of ideas from a variety of viewpoints in an environment of respect, collaboration, and fairness. We promote the principles of equity and inclusion within our department and beyond through recruitment and retention, graduate training, clinical work, research, service and teaching, as well as through open and productive dialogue. More broadly, the University of Delaware is also committed to inclusive excellence. The University of Delaware is an Equal Opportunity Employer which encourages applications from minority group members and women. The University's Notice of Non-Discrimination can be found at http://www.udel.edu/aboutus/legalnotices.html. Applications close: Open until filled

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Invalid license key error for Freesurfer 5.1
by An Lijun 25 Aug '19

25 Aug '19

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mri_vol2vol
by Rihana Rayan 25 Aug '19

25 Aug '19

External Email - Use Caution Dear FS users, I have performed recon-all on structural data and created ROIs (using mri_binarize), I want to mask functional data (GLM beta) with ROIs. To match the file sizes, I resampled the ROI.nii by performing the command: mri_vol2vol --mov ROI.nii --targ beta_01.nii --regheader --o ROI_in_beta.nii Multiplying ROI_in_mask.nii by GLM beta, results in NaN over some voxels. Can anyone help me solve the problem? Best regards, Rihana

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what is the right manual correction when ?h.white extends into gray matter
by Caroline Chwiesko 23 Aug '19

23 Aug '19

External Email - Use Caution Hello Freesurfer experts, I wrote a previous email about my issue that in many of my subjects I have spots where the ? h.white is extending too much into the gray matter after running recon-all. As I understood from a conversation from somebody else, [[Freesurfer] WM surface including too much gray matter], you are currently looking into whether default parameter adjustments in recon-all can fix this problem. Until then, it was recommended to edit those errors manually. My question is what editing technique should I use if I want to manually edit thesis type of errors? Removing the voxels that I think are gray matter from the white matter file using recon edit? I am a little confused about this because I noticed that the ?h.white boundary does not necessarily follow the wm boundary (see attached image), so I am wondering, if changes to the wm will fix the problem that I have. Thank you very much in advance! Carolin [image: Screen Shot 2019-08-06 at 1.32.16 PM.png]

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Freesurfer August 2019