Freesurfer February 2022

freesurfer@nmr.mgh.harvard.edu

83 participants
132 discussions

Unsure About Longitudinal & GLM Tutorials
by Edwards, Vincent 04 Feb '22

04 Feb '22

External Email - Use Caution Good morning Freesurfer Team! I would like to use GLM on my longitudinal study to measure change between two time points. I followed the longitudinal tutorial, and to my understanding, I would move on to the general glm tutorial next. The longitudinal tutorial says that "you can compare groups similar to a cross sectional analysis", but when we run stats on our significant clusters our results look "odd". I may have misunderstood the tutorial, but I plugged the longitudinal timepoints into my fsgd file like this: Input Subject1_TP1 subject 57 0.93 Input Subject1_TP2 subject 57 0.93 Input Subject2_TP1 subject 64 1.22 Input Subject2_TP2 subject 57 1.22 I'm not sure if what we ran is actually finding change between timepoints in our subjects. We happened across a glm paired-analysis tutorial. Should we re-run our data through that instead? The longitudinal tutorial only referenced the regular glm tutorial, so I want to make sure that we are following the correct steps - perhaps there is something I did wrong with my fsgd file? The paired-analysis tutorial seems like it may be appropriate, but I was hoping you could clear up our confusion before we move forward. Thank you, Vince

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lGI value aberrantly high, again
by Bernardoni, Fabio 04 Feb '22

04 Feb '22

External Email - Use Caution Dear all as some other posted before me, sometimes the computation of lGI fails with the message (see for example: https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiH…, https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9…, https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9…) 'lGI for vertex number 35901 of the outer mesh is 2.5958 ... remeasuring lGI value for vertex iV = 36001. It may take a few minutes. WARNING -- Problem for vertex iV = 36001, lGI value is aberrantly high (lGI=53.1127)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.' as many reported before me, computation of euler number gives 2, i.e. nothing wrong. another suggestion by marie schaer is to rerun recon-all -hemi ?h -autorecon2 -autorecon3 , with or without the -randomness option. The point is that the -randomness option seems to have no effect, the error occurs again in exactly the same place, with the exact same value (lGI=53.1127). I am using freesurfer 7.1. Has there been any development to solve this? Thank you in advance Fabio Bernardoni Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1xvuU9YpZrNAT8MBR8aeslCWdv2cNu-xhctWukMA-pgRDlf…; http://secure-web.cisco.com/18N9590xMz7PXy9R7etuq98MdgjKagN7Y04h0saKn6vRWYJ… +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswP… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswP… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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impact of defacing on eICV calculations
by Ritobrato Datta 04 Feb '22

04 Feb '22

External Email - Use Caution Hi All, I have inherited some T1 data that are defaced. If I run the defaced images through freesurfer, will that impact the eICV calculations ? Please let me know. Many thanks Ri

2 1

Display PCC in cluster
by Andrei Bieger 04 Feb '22

04 Feb '22

External Email - Use Caution Hi, Douglas, I performed a group analysis and, after permutation, one cluster survived. How can I display this cluster over an inflated surface, but with colors representing the partial correlation coefficient? In other words, I would like to see the pcc.mgh file in an inflated surface, but only for those vertices belonging to the cluster. -- Andrei Bieger

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Co-Registration after recon-all
by m-maiworm＠web.de 04 Feb '22

04 Feb '22

2 1

mri_normalize error MP2RAGE
by Dr. Cornelius Kronlage 04 Feb '22

04 Feb '22

External Email - Use Caution Dear freesurfer experts, when running recon-all (FS version 7.2.0) on skullstripped 3T MP2RAGE sequences, about 10-20% of scans from one scanner fail because of this: mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz [...] Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed Command exited with non-zero status 253 nu.mgz as the input to mri_normalize looks good to me. I am of course happy to provide full logs and some example data - please let me know. The exact same problem (also MP2RAGE data) has been described twice before, but I couldn't find a solution: https://secure-web.cisco.com/1r3_UfItk0odyQTEjL22mLAxycj89_vXfN--AkpFwUzred… https://secure-web.cisco.com/1_dIFX4W-YMl78kLd-J9E7AGEkpzUy7zCtCTsFt-L6nLdA… Thanks you in advance and best wishes Cornelius

3 3

Postdoc position is available in Photoacoustic Imaging Instrumentation - ASAP
by Nasiriavanaki, Zahra,M.D. 03 Feb '22

03 Feb '22

From: Avanaki, Kamran Sent: Tuesday, February 1, 2022 5:21 PM To: Avanaki, Kamran <avanaki(a)uic.edu<mailto:avanaki@uic.edu>> Subject: Postdoc position is available in Photoacoustic Imaging Instrumentation - ASAP Dear colleagues, I hope you are well and safe during this complicated time. We have a postdoc position available in the OPIRA laboratory in the University of Illinois - Chicago (UIC). I appreciate if you could kindly let your students and colleagues know about this position. Postdoc position in Photoacoustic Imaging Instrumentation. The postdoctoral fellow will contribute to the design, development and optimization of a photoacoustic tomography system for brain imaging. Some ofresponsibilities include conducting phantom and animal imaging experiments, as well as data analysis. This project is hosted by the Biomedical Engineering Department at UIC, collaborating with Biomedical Engineering Department at the University of Michigan and Harvard Medical School. Requirements for this position include: (a) a PhD in Electrical Engineering, Biomedical Engineering, Physics, or Biomedical Physics; (b) a strong background in design and development of imaging system instrumentation, especially optical and ultrasound imaging; (c) strong Matlab (required) and Labview programming; (d) ability to work independently and in a multi-disciplinary team environment; (e) experience with optical system design, machine learning and GPU programing are plus. The successful candidate will be expected to publish significant research findings and must have excellent verbal and written English communication skills. The candidate will be asked/trained in grant writing. Interested candidates are invited to email their detailed CV to Dr. Avanaki at avanaki(a)uic.edu<mailto:avanaki@uic.edu>. More details about the projects will be discussed during the interview. Thank you very much. Sincerely, ---------------------------------------------------------------- Kamran Avanaki, Ph.D. Associate Professor of Biomedical Engineering & Dermatology College of Engineering and School of Medicine The University of Illinois at Chicago (UIC) Scientific Member of Robert H. Lurie Comprehensive Cancer Center 851 S Morgan St, MC 063, Chicago, IL 60607 Tel: +1 (312) 413-5528 Lab URL: http://www.opira-avanaki.com/<http://secure-web.cisco.com/16VqK6Oy1dV4Nq-0apqyFymCLmO2pjujvDVpBr4vhtkA5vA…> Google Scholar: https://scholar.google.com/citations?user=fGi2vFMAAAAJ&hl=en<https://secure-web.cisco.com/1qojCuPTC_rh5o55Vk2brQTme7JwWqihPg59fxDqLYFyxt…>

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Postdoctoral position open at the University of Geneva
by federica ribaldi 03 Feb '22

03 Feb '22

External Email - Use Caution Dear Freesurfer users, Prof Garibotto’s group, Laboratory of Neuroimaging and Innovative Molecular Tracers ( https://secure-web.cisco.com/1jdhij-eXsg6D42Zh_F9Z60qblp8WlmxcT2P_hYVeukiqs…) University of Geneva, Switzerland has an open postdoctoral position to contribute to the scientific research in the field of Alzheimer’s Disease (AD) and cognitive disorders, focusing on clinical and neuroimaging analyses (mainly PET and MRI) combined with genetic and biofluids data to define and model disease characterization and progression. More information about our group, the call and application link can be found here: https://secure-web.cisco.com/1shidNyFyiWcXFItxhfNkc8ENHXzAl0HDMt2Y_VOOzvXYf… Feel free to distribute this announcement to potentially interested people. Best, Valentina Garibotto

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Postdoc position at the University of Delaware: infant + adolescent fMRI, ANS, EEG
by Korom, Marta 02 Feb '22

02 Feb '22

External Email - Use Caution Postdoc with Mary Dozier's Attachment and Biobehavioral Catch-up Lab January 24, 2022 The Attachment and Biobehavioral Catch-Up (ABC) Lab, supervised by Mary Dozier at the University of Delaware (UD), is looking to hire a postdoctoral fellow. The position involves working on one of two randomized clinical trials (RCT) that test the efficacy of an early home visiting intervention (ABC). In one of the RCTs, mothers using opioids and their infants are currently being enrolled. Autonomic nervous system regulation, brain activation (using event related potentials and MRI), cortisol regulation, DNA methylation, attachment, and behavioral regulation are among the variables assessed. The second study assesses adolescents who were first enrolled in an RCT in infancy. All adolescents are scanned at ages 13, 14, and 15, and additional behavioral constructs (inhibitory control, emotion regulation, attachment/affiliation) are assessed. The postdoctoral fellow will be responsible for overseeing research activities. Prior experience with MRI data collection and processing is preferred but not required. This is a full-time benefited position. Salary will follow the NIH postdoc salary scale. Ph.D. required by position start date, preferably in Clinical Psychology, Developmental Psychology, Behavioral Neuroscience, or related field. Strong organizational and interpersonal skills are essential. The position start date is flexible, with a preferred start date in the spring or early summer of 2022. Please send CV and letter of interest to Mary Dozier, mdozier(a)udel.edu. More information about the ABC Lab can be found at http://secure-web.cisco.com/1ZTIbTpjH9xQmnw0jjuklLDV1Tav0r5BUlVZbIeqDHOc3ZF… -- *Marta Korom | *PhD Candidate University of Delaware, Clinical Science e-mail: mkorom(a)udel.edu phone: 646 861 8461 http://secure-web.cisco.com/1ZTIbTpjH9xQmnw0jjuklLDV1Tav0r5BUlVZbIeqDHOc3ZF…

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segmentation of thalamic nuclei
by Marie Drottar 02 Feb '22

02 Feb '22

External Email - Use Caution Hello; I am having trouble with this functionality completing. It appears that MATLAB exits because of a fatal error. I am attaching the log file that was created. thank you Marie

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Freesurfer February 2022