Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Freeview Update using MAC
by Erika Nolan 19 May '21

19 May '21

External Email - Use Caution Good afternoon, I downloaded Freesurfer 7.1.1 and am trying to open HCP .gii files in Freeview. I tried updating Freeview (https://secure-web.cisco.com/1veSBR5ECpngEulfhl0eWcwLxUmMQ4QR1JG2qWSdPD48G1…) using the instructions for MacOS but it fails: Mac 1. Go into your $FREESURFER_HOME and create a backup of your existing freeview app (this may require sudo access): cd $FREESURFER_HOME cp Freeview.app Freeview-backup.app 2. Download the dev, standalone freeview tarball from here<https://secure-web.cisco.com/1-rTW8L4qktbL8zcQ8YGBhA2846k3Po3bbKwIzxjkbPFAK…> 3. Untar freeview within your $FREESURFER_HOME (this may require sudo): cd $FREESURFER_HOME tar -xzvf /path/to/freesurfer-darwin-macOS_HighSierra-dev-freeview.tar.gz 4. IMPORTANT: If you are replacing freeview in a freesurfer release LESS than 7.0, then you must also remove the line "source $FREESURFER_HOME/sources.csh" from the $FREESURFER_HOME/bin/freeview script The tar file that downloads is " freesurfer-darwin-macOS-dev-freeview.tar" is this file correct? My Mac is a MacOS Sierra (not HighSierra), version 10.12.6. Is it possible for me to get a file that is compatible with my Mac? Thank you for your help!!! Erika

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SUIT cerebellum parcellations
by Erik O'Hanlon 19 May '21

19 May '21

External Email - Use Caution Dear FS Experts, Just wondering if it's possible to use the SUIT labels in the LUT to obtain cerebellar quantification measures and also to make masks for tractography specific to each area? Thanks in advance Erik

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C.Thickness: Statistical analyses with three groups
by Steve Petersen 19 May '21

19 May '21

External Email - Use Caution Dear Freesurfer experts, My goal is to compare the cortical thickness between three groups. For that purpose, I performed whole brain analysis with a F-contrast to evaluate a group effect. Since the F-test was significant, I performed pairwise comparisons to evaluate the direction of these differences. However, I noticed that some brain areas that are significant in one pairwise comparison (that are consistent with our hypothesis) were not significant in the F-test. I am a bit lost about how to proceed in this situation, can I report significant results in the pairwise comparison that were not previously significant in the F-contrast or do I need to perform the pairwise comparisons by applying a mask to the brain areas where there were significant results in the F-test? Apologies for asking this simple question, I am a beginner in statistical analysis with MRI data. Thank you very much for your help. Best regards,

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Postdoctoral position open at the University of Geneva
by federica ribaldi 17 May '21

17 May '21

External Email - Use Caution Dear Freesurfer users, Prof Garibotto’s group, Laboratory of Neuroimaging and Innovative Molecular Tracers ( https://secure-web.cisco.com/1f690DlehlIiGMbMNMyi9vyUen43cL9dNElX6oldhDASYv…) 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/1POXw5qHPPSUhfiRwFc3DD62M6qjUjqrAu1zkbeJ3GIvI2… Feel free to distribute this announcement to potentially interested people. Best, Valentina Garibotto

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Sulcus represented in wm.mgz filled in lh.white
by Dierker, Donna 17 May '21

17 May '21

External Email - Use Caution Hi freesurfer experts, I have some cases where sulci near the occipital pole are reflected in the wm.mgz, but are filled in the white surface. Attached is a capture showing the sulcus near the image center, where the crosshairs are located. Might the topology fixer have filled in this sulcus, to reduce topological errors? This was generated using recon-all -all, freesurfer 6.0, ubuntu 18.04.3. Thanks, Donna ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Overlay of MGH clusters on Broadmann atlas
by Romanella,Sara (BIDMC - Wilkinson - Neurology SF) 16 May '21

16 May '21

Hi FreeSurfer community, I have a cluster.mgh file (along with the .annot and .summary) resulting from correlation analysis of cortical thickness in a group of patients. I can open it as overlay in freeview but I was wondering if there was any chance to overlay it to a Broadmann atlas (hopefully in freeview) so I can visually show the overlap of the clusters with the BA areas. I cannot seem to find a Broadmann atlas in fsaverage to open in freeview. Also I was wondering, if I want to convert .mgh and open it on Connectome Workbench what extension do you think I should use (e.g., .gii). Should I use mri_convert or mris_convert? I am not sure if .mgh should be converted as a surface. Thank you so much for your help! Sara ? Sara Romanella Fellow (Ph.D. in Neuroscience) Berenson-Allen Center for Noninvasive Brain Stimulation Department of Neurology | Beth Israel Deaconess Medical Center 330 Brookline Avenue, 02215 Boston, MA, USA Phone Nr: +1-339-229-7645 ________________________________ 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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How to use atlas AAL3 label on Freesurfer?
by Diógenes Bispo 15 May '21

15 May '21

External Email - Use Caution Hi Freesurfer team I would like to know how I convert an AAL3 atlas label to the standard Freesurfer space. In addition, I would like to extract volume and cortical thickness from the subjects in this region of interest. I am using Freesurfer version 7.1.1. Atlas AAL3 (https://secure-web.cisco.com/1tq7UWlhNLqqLMlQ1A0WbA7mUYazrixorG3fe8eaD1j3rn…) Thanks. Diógenes diogenesdiego(a)gmail.com

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Cerebellum Segmentation
by A.R. Sekar 15 May '21

15 May '21

External Email - Use Caution Hello Experts! This is the first time I am doing tractography and my aim is to do it specifically for the cerebellum. I saw online that FreeSurfurer can segment the cerebellum, to create the ROI but I’m not entirely sure how to go about this. So far I have done the pre-processing, co-registration onto diffusion space and created FOD. I have also ran recon all on my structural data. It would be great if you could give me advice and any feedback about the pipeline. Thanks for your help! Regards, Akila

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FreeSurfer Error: xx: Subscript out of range
by Shanika Jayakody 14 May '21

14 May '21

External Email - Use Caution Dear FreeSurfer team I have been trying to run trac pre-processing on some subjects but keep getting the error "xx: Subscript out of range." The number of data entries in bvecs/bval files are similar to the .nii file and I have used configuration files similar to the ones I have been using Attached here are my configuration file and trac-log file. Any suggestion/advice is really appriciated Thank you Regards Oshadi

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Re NEUROIMAGINGPOSITION IN EPILEPSY Available
by Xiaozhen You 13 May '21

13 May '21

External Email - Use Caution *NEUROIMAGING POSITION IN EPILEPSY* *AT CHILDREN’S NATIONAL HOSPITAL AND THE GEORGE WASHINGTON UNIVERSITY* A position is available starting *Spring/Summer 2021* in the Comprehensive Pediatric Epilepsy Program at Children’s National Hospital affiliated with George Washington University in Washington DC (Polerlab.org <http://secure-web.cisco.com/1Y4lk4CR_HLS6scGFa1DcCuY-aG2PbH_t2oHL0ieCABcIRd…>). This position involves the application of state-of-the-art functional and structural MRI imaging methods applied in clinical research. The candidate will apply methods previously developed but not used in epilepsy as well as develop novel computational imaging methods. Our aim is to apply sophisticated approaches to answer clinical questions (e.g, identify seizure focus; develop sensitive MRI metrics of cognitive reorganization; examine pre- and post-surgical changes structurally and functionally to build sensitive predictive models). The candidate will have the opportunity to initiate his/her own research projects, mine existing data, and collaborate with a multidisciplinary team including neurologists, neurosurgeon, neuropsychologists, fellows, graduate students, and undergraduate research assistants. Candidate qualifications and educational background are flexible and the position will be tailored accordingly. We prefer a postdoctoral level; however, will consider an advanced graduate student. An early career faculty position is an option as well. Appointments are for two years minimum, renewable upon mutual agreement. Candidates should have graduate school training in engineering, neuroscience, computational, or other biological sciences. Experience with computer programming and image processing is essential. Familiarity with fMRI analysis software including SPM, FSL, AFNI, and Freesurfer, as well as programming environments such as MATLAB or Python is highly desirable. Children’s National Hospital is an equal opportunity employer. Full-time employees receive full benefits, competitive salaries, and excellent resources for career development. To apply, please send a letter describing research interests and experience, curriculum vita, and names and contact information of three references to William Gaillard, MD at wgaillar(a)childrensnational.org and Madison Berl, PhD at mberl(a)childrensnational.org.

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