Freesurfer March 2021

freesurfer@nmr.mgh.harvard.edu

106 participants
144 discussions

Problem with freesurfer measures
by Alberto Del Cerro Leon 06 Apr '21

06 Apr '21

External Email - Use Caution Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures: 1. Gray and White Matter Volume 2. Folding Index 3. Curvature measures 4. Thickness However I don't know what surface in the surf folder of each subject I have to use. Could u help me?

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fMRIPrep BOLD Output
by Karan Desai 06 Apr '21

06 Apr '21

External Email - Use Caution Hi Freesurfer List, I am running fMRIPrep and getting the first two FS output files (aseg and aparcaseg seen above in the screenshot), but not the actual file I need which is the one where it is resampled to the mesh. I have run fMRIPrep and have those two files except the actual BOLD series resampled to the surface mesh. Is there a FS command that can be used to do that one step? Best, Karan

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quantification of volume of perivascular spaces
by Antonín Škoch 05 Apr '21

05 Apr '21

External Email - Use Caution Dear experts, We would like to quantify volume of brain perivascular spaces. Ideally longitudinally - i.e. to study the dynamics of perivascular spaces in multiple measurement of the same subject. Is it possible to use samseg for this? Do you think, that --lesion flag in samseg would work estimation of perivascular spaces? Or other setting of samseg will be better option? Or, would you rather recommend other tools? Any idea/comment will be greatly appreciated. Regards, Antonin Skoch

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Subthalamic nucleus volume
by T. Pansuwan 05 Apr '21

05 Apr '21

External Email - Use Caution Dear Freesurfer experts, As part of my project, I would need to have subthalamic nucleus as one of my ROIs in which this is not available by Freesurfer. I found a probabilistic subthalamic nucleus atlas in FSL atlases (in MNI152 space) and thought I would convert this to fsaverage space. I have attempted: mri_label2vol —reg $FREESURFER_HOME/average/mni152.register.dat —seg STN-maxprob-thr25-0.5mm.nii.gz —temp $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz —o STN_mni152_in_mni305.nii.gz But the location was much more dorsal than original, 1) I was wondering if there are alternative methods I should try and what could have been the problem? At the end, I hope to obtain individual subject’s subthalamic nucleus volume, 2) I was wondering how to convert volume in fsaverage space to labels in fsaverage space so that I can convert the labels to native space? Thank you so much! Tanrada Pansuwan

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ERROR: Cannot find stats file
by atacan zeybek 05 Apr '21

05 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to create a text file of amygdalar nuclei of given subjects. I use this command: asegstats2table --subjects 8070 8071 8077 --statsfile=amygdalar-nuclei.lh.T1.v21.stats --tablefile=amygdalarnuclei.lh.T1.v21.txt –skip And get an error like this: ERROR: Cannot find stats file /home/atacan/Desktop/freesurfer/subjects/8070/stats/amygdalar-nuclei.lh.T1.v21.stats Unfortunately I can't search the mail archives because I get an another error while loading the page. Freesurfer version: CentOS 7 x86_64 (64b) tar archive Platform: Ubuntu 20.04.2 LTS

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functional to anatomical registration question
by Nasiriavanaki, Zahra 05 Apr '21

05 Apr '21

Dear Freesurferers, I have a question and I appreciate it much if you could please reply. I need to know how to check subcortical functional to anatomical registration. I know for checking the cortical registration I can use the below command: tkregister2 --s $subj --mov template.nii.gz --surf --reg init.register.dof6.dat Could you please tell me what command should I use to check the registration in subcortex? Thanks MOna Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Boston, MA, USA, 02129

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Running recon-all with FLAIR
by Edina Szabó 05 Apr '21

05 Apr '21

External Email - Use Caution Dear All, We are running recon-all on the latest version of FreeSurfer (v7.1.1). We are using both T1 and FLAIR images to better define the pial surfaces, but when we run the recommended command line (recon-all -subject subjectname -i /path/to/input_volume -FLAIR /path/to/FLAIR_volume -FLAIRpial -all) the pial surface is very underestimated (?.pial.FLAIR – and the aseg volume is based on these surfaces), and we get better results without the FLAIR. It seems that FreeSurfer mis-registers the FLAIR to the T1 during the process. Is there a separate step we should do to register FLAIR to T1? Thank you, Edina

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Left-Right labeled brain MRI
by Arman Avesta 31 Mar '21

31 Mar '21

External Email - Use Caution Hi, Thank you again for responding to my previous questions! I'm writing a python class to show MR images, and I need to have one brain MRI volume (e.g. nifti or mgz) in which left and right are labeled in some way. FSL website used to provide a test MRI volume that was labeled: Unfortunately I can't find this volume on the internet anymore! So I need help :) Thank you,Arman

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Research Assistant/Lab manager position at Brown
by Hwamee Oh 31 Mar '21

31 Mar '21

External Email - Use Caution A full-time Research Assistant position is available in the Oh Laboratory for Cognitive and Translational Neuroscience in the Department of Psychiatry and Human Behavior at Brown University. This position entails both administrative and research responsibilities. The candidate will be responsible for recruiting and screening participants, maintaining participant records (e.g., consent forms, screening forms), assisting with the supervision and training of undergraduate students, and assisting day-to-day oversight of study maintenance. The Research Assistant will assist with ongoing behavioral/experimental, neuropsychological, and neuroimaging (fMRI and PET) data collection, image and non-image data management and quality control, and data analysis and manuscript and data preparation The lab uses state-of-the-art cognitive neuroscience and multimodal neuroimaging methods to study neurocognitive mechanisms of visual memory and how they change with brain aging and Alzheimer’s disease pathology in cognitively normal older adults. The Oh laboratory is part of the Memory and Aging Program (MAP) at Butler Hospital, one of the leading clinical research centers for Alzheimer’s disease in the United States. The laboratory is also affiliated with the Carney Institute for Brain Science and Department of Cognitive, Linguistic, and Psychological Sciences at Brown University, providing a rich and collaborative training and research environment for innovative cognitive and brain science with clinical applications. This is a fixed term position with a current end date of 05/31/2022 which may be extended based upon available funding. Start date is ideally between April 1, 2021 and June 30, 2021 with some flexibility. *Education and Experience* *Required:* · Bachelor's degree in psychology, neuroscience, cognitive science, computer science or a related field and 1-2 years of experience in a related field · Experience in programming (e.g., in Python, MATLAB, bash, R, Psychopy), analysis of human neuroimaging data, and familiarity with statistics are desirable. *Preferred:* · Research experience with data collection in human subjects. *Job Competencies* · Must possess excellent communication and strong organizational skills. · Must demonstrate the ability to work independently as well as in a team setting. · Flexibility in scheduling is also required (e.g., willingness to occasionally work week nights and weekends to accommodate participant schedules). · The candidate will have no contraindications to entering Zone 4 of a 3T MRI scanner. · The Research Assistant must provide their own transportation between research sites. · Possesses a willingness and ability to support a diverse and inclusive campus community. The position is open to international applicants who have already acquired legal status for working in the U.S. For interested individuals, please apply through this website: https://secure-web.cisco.com/1ebuUeCtr5kVx--Ak98g0Z8Dpb-C-hr32lB68G879Th05d…. For inquiries, please contact Dr. Hwamee Oh (hwamee_oh(a)brown.edu) for more information on the position.

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Export stats: HCP Multi Modal parcellation
by Miguel Ángel Rivas Fernández 31 Mar '21

31 Mar '21

External Email - Use Caution Dear Freesurfer experts, it is possible to export the stats of subjects reconstructed with freesurfer v.6 using the HCP Multi Modal parcellation? (Glasser et al., 2016). Thank you in advance. Best regards, -- *Miguel Ángel Rivas Fernández*

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Freesurfer March 2021