Freesurfer

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30081 discussions

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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Infant Freesurfer exiting without error
by COLLEEN PLETCHER 13 May '21

13 May '21

External Email - Use Caution Hi, I am trying to run infant freesurfer using the --segfile and --masked options. When I attempt to run it, it runs for a bit and then I get this: USAGE: mri_or <options> fname1 fname2 .. After this, the program exits. I am not getting any error, so I am confused about why it is exiting suddenly? Thank you very much! -Colleen

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Sulcal probability maps
by Kristi Drudik 12 May '21

12 May '21

External Email - Use Caution Good afternoon, I hope this email finds you well. I am in the process of "painting" MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I: * Painted the sulcus of interest on the surface by creating a .label file. * Registered this .label file to fsaverage (mri_label2label) * Converted the .label file to vol (mri_label2vol) * Converted it to a surface file (mri_vol2surf) * Concatenated the data to create an average (mri_concat --mean) * Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage? Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi Kristi Drudik Ph.D. Student, Clinical Psychology Montreal Neurological Institute McGill University Montreal, Canada

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Cluster correction at subject level using -log10(p) values
by Leonardo Tozzi 12 May '21

12 May '21

External Email - Use Caution Dear Experts, I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file. I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my inference to a ROI. I have a few questions. First of all, is it correct that I should to a -log10(p) transform on my p values before entering them in mri_surfcluster? Second, will the csd generated by mcsim be valid to feed in mri_surfcluster since the values are a -log10(p) transformed? Does mcsim -log transform the gaussian noise it uses at some point or is this not necessary? My calls to the two methods are as follows (for one hemisphere): First the mcsim: mri_mcsim --o “${subject}_mcsim_lh_${roi}" --base mc-z --surface ${subject} lh --nreps 10000 --label $roi Then the mri_surfcluster: mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \ --csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \ --clabel "${subject}/label/lh.${roi}.label" \ --cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \ --vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \ --sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \ --thmin 3 \ --surf white \ --subject ${subject } \ --hemi lh \ --ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \ --cwpvalthresh 0.05 In the call of mri_surfcluster, I want a cluster forming threshold of p=0.001, which would correspond to -logp(0.001)=3. Is it correct that the argument --thmin should be expressed as -log10(p) but the parameter cwpvalthresh should be p? The reason why I think I did something wrong is that I get a lot of clusters from this analysis, sometimes >15 per individual. This makes me think that the correction might not be as stringent as I would like to. Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi(a)stanford.edu<mailto:ltozzi@stanford.edu> | (650) 5615738 Connect with us! [signature_1075933358]<https://secure-web.cisco.com/154LqJFzFLISeYtGLsUgwToWD-mN0G4thIfubhtThzJ6F9…> [signature_1282923475] <http://secure-web.cisco.com/11JA0cps0LSyc_YKkvLkjj53ioS8G144vcOsjQghqMz-F2M…> [signature_911042299] <https://secure-web.cisco.com/1Mkao1uevqs0RL-8o0FG2efSSKGQAOwrHeahbv3dcsTbir…>

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