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Research Specialist - UW- Madison, WI (Center for Healthy Minds)
by CHM Recruiting 18 Oct '21

18 Oct '21

External Email - Use Caution Research Specialist, UW- Madison, WI, Center for Healthy Minds Are you interested in how emotional and brain processes are related to life experiences, cognition, health, and well-being? The Research Specialist will be responsible for scientific integrity of data collection, data cleaning, and data processing for the Emotion and Wellness Study, led by Dr. Stacey Schaefer, at the University of Wisconsin-Madison's Center for Healthy Minds. Data collection includes in-person study visits, working with a participant one-on-one collecting a variety of questionnaires, cognitive/behavioral tasks, biomarkers (e.g. saliva and dried blood spots), psychophysiology (e.g. facial electromyography, heartrate, respiration and skin conductance), and neuroimaging (e.g. functional and structural MRI). This position requires good people and communication skills, and flexibility to work with people from a wide age-range and different backgrounds. Opportunities exist to learn a variety of data processing techniques and skills. Please go to https://secure-web.cisco.com/1Zf73pYY8VMjVLZS11Db1pOKksXzIz1b_4QF0Nrxlz5im_… to view the complete job posting and apply online. Deadline to apply is November 2, 2021. UW-Madison is an affirmative action/equal employment employer and we encourage women, minorities, veterans, and people with disabilities to apply.

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Topological error on recon after manual edits
by M Pope 18 Oct '21

18 Oct '21

External Email - Use Caution Hi all, I ran recon-all successsfully on a subject. I then did some manual edits on both the brainmask (removal of dura) and wm and then ran recon again for the edits. This usually works fine, however for one subject the recon (after edits) fails because of time limit on my process. It gets stuck on the fix toplogical errors stage, as there is a defect with 36000+ vertices included. I looked at the lh.inflated.nofix and lh.orig.nofix and indeed you can see there is a lot of dura/skull being included in the surface on the lh. However, recon did work just fine the first time where these did happen, and the final surfaces look fine (the manual edits I did were few!) Gcut also does not work because it removed too much of the temporal areas and the cerebellum. Are there any suggestions on how to fix this without having to go in and manually remove all the dura (it is a lot!). I attach the recon.all log so you can see how the first recon ran (without errors) and then after edits where it fails. Could I perhaps use the -nofix flag? Thanks, Marianna

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mri_surf2vol with inflated surfaces
by Nicolas Munera Garzon 18 Oct '21

18 Oct '21

External Email - Use Caution Greetings freesurfuer community, I've been working on a research project for which I need to simulate different levels of inflation for a given brain MRI, to achieve so I have tried the following so far: 1. To run recon-all for a test subject 2. To run mris_inflate over pial surfaces (as that's the structure I need for my simulation) 3. To try to get back to a .nifti file by using mri_surf2vol. However I have been unsuccessful with this step as the required --ribbon parameter refers to ribbon.mgz which is a binary mask of segmented tissue. My question: is there a way for me to generate a ribbon.mgz with the inflated brain, or does anyone know how to get an inflated version of the brain that I can use as an actual volume / image (.nifti, .mgz...)? Thanks in advance! -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web http://secure-web.cisco.com/12-1T4t5I3WmZta2EqCjvwIWHtQeGJkmeNAZoRBbnrgdUpK… <http://secure-web.cisco.com/1ggE-ylwUekBVUwUxvozHFy8vy00YXExkO6K6A3ePYD9meH…>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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ACPC alignment before processing
by Zhengchen Cai 18 Oct '21

18 Oct '21

External Email - Use Caution Hello FreeSurfer Developers, I wonder if we have a function that could automatically align T1w to ACPC before running recon-all? Or if we have an option in recon-all that could do this ACPC alignment automatically? I noticed there are such ways after running freesurfer by applying the transformation matrix, but I guess it will be less convenient than pre-alignment since we don't bother to transform all the output. Especially if we use freesurfer with other tools like fMRIPrep, all functional images will also be registered to ACPC aligned T1w. I ask this since sometimes the T1w is tilted and not desirable for visualization purposes. Thanks a lot. Best regards, Zhengchen

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Different pixel spacing for scans in the same cohort
by Castro Leal, Gonzalo 18 Oct '21

18 Oct '21

External Email - Use Caution Dear Freesurfer, I was wonderign wether processing scans and comparing their stats, e.g. cortical thickness and area, could be not recommended if the pixel spacing across all the scans was different, i.e. the range is between .9375x.9375x1.2 and 1.3542x1.3542x1.2. Many thanks, Gonzalo.

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MEMPRAGE protocol
by nicola spotorno 18 Oct '21

18 Oct '21

External Email - Use Caution Dear all, I read on the FAQ that MGH would kindly share an optimized MEMPRAGE. I was wondering how/how should I get in touch to discuss about this option. All the best, Nicola

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Job Posting - Center for Healthy Minds
by CHM Recruiting 18 Oct '21

18 Oct '21

External Email - Use Caution Hello, Would you please list the attached on the Freesurfer (listserv): Research Specialist - UW Madison, WI - Center for Healthy Minds. Thank you, Lisa Wesley Human Resources Generalist Center for Healthy Minds lawesley(a)wisc.edu

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Creating a surface parcellation from a volume atlas
by Paul Dhami 18 Oct '21

18 Oct '21

External Email - Use Caution Dear Freesurfer community, I have a .nii volume atlas (CAREN), defining 5 networks, in MNI (ICBM152) space. However, I wish to do my analysis in surface rather than volume space, and for the software I am using, that means I need to load in a .annot file. For the first step, I used: mri_vol2label --c CAREN_5networks.nii --id 1 --l 1.label and did this for values 1 to 5 (for each of the networks). However, looking at the resulting label file, the first column is nothing but -1 values. I believe this should be the vertex number, and trying to combine these labels into an .annot file is not working. Apologizes for the naive question, but can anyone share as to how I can ultimately create a surface atlas when I have the volume.nii atlas file? Was I wrong with mri_vol2label as my first step? I am using Freesurfer version 7.2.0. Thank you, Paul

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Question about 'thickness.fwhm10.fsaverage'
by Dongyue Zhou 18 Oct '21

18 Oct '21

External Email - Use Caution Dear FreeSurfer experts: I use the 'qcache' command to get the file '$SUBJECTS_DIR/subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh'. Now,I have known that cortical thickness in this file is in standard space.But I don't understand why it is an average of 40 subjects. Is it not CT measures an individual in standard space? I can get cortical thickness in each vertice by reading this file in matlab. And I know mean CT is computed by dividing sum CT of all ROI vertices by the number of ROI vertices. Is there any way I can get individual ROI in standard space if I want to compute mean CT measures of each ROI? or Can I use file '$SUBJECTS_DIR/fsaverage/label/?.annot' as atlas directly?

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Problem with intensity normalization control points
by Staci A Board 18 Oct '21

18 Oct '21

External Email - Use Caution Hello, our lab has been using freesurfer for years, dating back to version 4.3 and recently ran into a problem with a new installation of 7.2. After adding control points in the typical fashion and saving them into the subject’s tmp folder as “control.dat” and running -autorecon2-cp, mri_normalize seems to correctly identify the control points, the correct number, the mean value and the scaling. The subsequent steps complete without failure and brain.mgz is generated with 110 values in the cp spots. However, the subsequent wm.mgz and brainmask.mgz images do not seem to have been affected by the control points (e.g. the control point locations aren’t at a 110 value and the white matter is almost identical). Curious if anyone else has run into the issue? Is there a new workflow in this version of Freesurfer that I’m neglecting? So far I have tried to create a new control.dat using freeview and copied the old points into that file, and run twice with the same results.

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