Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

mri_error_no_clear_message
by Fargol Rezayaraghi 02 Jan '24

02 Jan '24

External Email - Use Caution Hi FreeSurfer Team, I hope this email finds you well. I'm trying to use a T1 image to get the aparc+aseg and wmparc nifti files. I was using this command: recon-all -s Subject1 -i T1.nii - all -notal -check ( I used recon-all -s Subject1 -i T1.nii - all first, and after getting Talairach error, I added -nota -check at the end). I'm getting following messages without clear error number: recon-all -s Subject1 exited with ERRORS at Thu Dec 14 21:18:02 EST 2023 For more details, see the log file /home/developer/Desktop/freesurfer/7.2.0/subjects/Subject1/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1cQznhKx0XPPZTJqsioLqCSeP_2I8A9nJBXfsYwGFwxBXmD… The version of the freesurfer: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b My platform is ubuntu 18_04_06 on Oracle VM VirtualBox I've attached the log file. -- Kind Regards, *Fargol R. Araghi (Rezayaraghi)* Ph.D. Candidate, University of Washington Department of Mechanical Engineering http://secure-web.cisco.com/1etf29AnmyfO7JDA1iwX4HvYcM0WXmMMFv-FG5QUpvlXzXt… <https://secure-web.cisco.com/1OE6aYFeTkmWM7FGsUCe4yHngfS6aQZieqg2uFkxfDu0qu…>

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RA Position Human Brain Mapping Lab
by Winfield, Jalen 02 Jan '24

02 Jan '24

External Email - Use Caution The human intracranial EEG Laboratory at The Feinstein Institutes for Medical Research - Hofstra Northwell School of Medicine in New York is looking for a research assistant with a start date as soon as possible. The successful candidate will help with the lab's research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterization of macro-scale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as invasive stereo EEG and electrocorticography recordings (iEEG, ECoG), anatomical MRI, fMRI, DTI, and direct electrical brain stimulation. The responsibilities will include assisting with the collection and analysis of the aforementioned data, project management, assistance with grant applications and progress reports, help with analysis of neural and imaging data using existing scripts (Matlab, Python), further development of those scripts (depending on coding and signal processing proficiency), and helping to present lab findings at conferences and in journals. The relative weighting of responsibilities can be adjusted depending on the interest of the applicant. If there is interest, the RA will have a scientific project with dedicated time to work on. Past research assistants have presented their work at clinical and basic research conferences, co-authored publications, and are working on first-author publications. They have gone on to medical schools or PhD programs after spending 1-3 years in the lab. This unique position will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. The location of the institute allows living either in the suburban neighborhoods of Long Island or in vibrant Brooklyn or Queens. Some employees also commute from Manhattan. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. ------------- Qualifications ------------- Minimum: - B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) - 2-year commitment - Experience with at least one programming language (MATLAB, R, or Python) Desirable: - Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data - Previous experience working with patients - Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation For more information about the position please send your CV along with your questions to Dr. Stephan Bickel (sbickel(a)northwell.edu<mailto:sbickel@northwell.edu>). Looking forward to hearing from you! The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Longitudinal pipeline with multiple scans at one time point
by Annchen Knodt 02 Jan '24

02 Jan '24

External Email - Use Caution I have a dataset consisting of individuals scanned at two time points 7 years apart. At the first time point, a single MPRAGE scan was collected for each individual; at the second, the same MPRAGE scan was collected, as well as an additional set of 4 shorter MPRAGE scans (collected with the aim of increasing measurement reliability). I’m looking to determine the best way to model the data with the longitudinal pipeline in order to detect reliable change between the two time points (there is test-retest data in a subset at both time points for assessing this). I’m specifically wondering whether it makes sense to compute a base “template” using all 6 scans from a given individual at once (i.e. the matching MPRAGE from tp1 and tp2 + the 4 short MPRAGEs from tp2). My intuition is that doing so would bias the template toward tp2 given that 5/6 images are from that time point, which is undesirable. I am also not sure how the different acquisition types affect things, as the shorter scans do produce systematically [slightly] different measurements. The plan is rely primarily on residual change scores for these analyses, to account for the slight differences in the acquisitions. Any thoughts / suggestions are appreciated – thanks! Annchen Knodt Research Associate Laboratory of NeuroGenetics Duke University

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Freesurfer/Freeview Version Compatibility
by Edwards, Vincent 01 Jan '24

01 Jan '24

External Email - Use Caution Hi, I'm following up on my quick question from this time last week. I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point edits, would I be able to do recon-all through Freesurfer 7? Years ago, someone asked if they could do recon-all in an older version of Freesurfer and edit in a newer GUI. Doug said that was fine. My question is basically the inverse of their problem. I assumed that since Freeview is a GUI, the version used shouldn't have any actual impact on things as long as we returned to version 7 to recon-all. I just want to confirm that my assumption is correct? The pipeline would be: F7 (recon-all), F5 (edit with freeview), F7 (recon-all for pial/wm/cp's) Thanks, Vincent Edwards

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Statistical Characteristics of Segmented Fornix from T1-w MR Images
by Ahsan Ali 01 Jan '24

01 Jan '24

External Email - Use Caution Dear Sir/Madam, I have segmented T1-W MR images from the ADNI database using Freesurfer. From aseg.nii, I have estimated the fornix structure (label number 250). I tried many times to get the characteristics of these structures but couldn't. It would be helpful for me; kindly let me know. File name "fornix.nii" at label 250. Its statistical parameters, such as fractal dimension, volume, mean, etc With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552

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Case-controls study !
by Martin Juneja 01 Jan '24

01 Jan '24

External Email - Use Caution Hello FreeSurfer experts, In my case-control study, I have a dataset of 5 healthy controls (HCs) and one patient (PAT). I was wondering if there is any way to perform GLM for PAT > HCs on brain morphometry data. When I tried to follow instructions from here: https://secure-web.cisco.com/1og9s8_rd4Lyx1NIwR7d0GRha020qNYi0MbIToxO7mZZ68…, the mri_glm fit command gives me the following error: Class Size and Means of each Continuous Variable 1 HC 5 24.2000 0.6000 2 Tumor 1 50.0000 1.0000 ERROR: Class Tumor has 1 members. With 2 variables and using DODS, you need at least 3 members It seems at-least three subjects are required in the Tumor category - because I have age and sex covariates in my fsgd file. I was wondering if there is any way to still perform the above GLM analysis or any other alternatives available to compare HCs vs one PAT. Thanks!

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mri_cc question
by Dawn Matthews 01 Jan '24

01 Jan '24

External Email - Use Caution Hello Freesurfer team and thank you for your continued responses to questions. My questions pertain to mri_cc, and subsegmentation of the corpus callosum. In prior runs of version 6.0, it seems that aseg outputs the subregions of the corpus callosum. The option for mri_cc also identifies those segments, and (Question 1) I wondered if in version 7.4 how that differs from what aseg normally outputs? In addition, (Question 2) with the -f flag to include the fornix, does this mean that the fornix is incorporated into the five subvolumes, or is the fornix volume calculated separately? (Question 3), For the option to set a different number of segmentations, how does that translate into the five ‘default’ segments (e.g. Anterior, Mid-Anterior, Central, Mid-Posterior, Posterior). Again, thank you for the team’s continued work.

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Freesurfer/Freeview Version Compatibility
by Edwards, Vincent 01 Jan '24

01 Jan '24

External Email - Use Caution Hello, I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point edits, would I be able to do recon-all through Freesurfer 7? I assumed that since Freeview is a GUI, the version used shouldn't have any actual impact on things as long as we returned to version 7 to recon-all. That seemed to be the case when someone asked a similar question (the reverse) <https://secure-web.cisco.com/1T0BQhB8dtRKrnTUmjN8XbkGqwEO9_yqoJso_TElGy705p…> , but that was many years ago so I wanted to confirm. Thanks, Vincent Edwards

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FW: Boundary based registration
by Spapens, Jeltje (NP) 01 Jan '24

01 Jan '24

External Email - Use Caution Hello Freesurfer developers, I want to register an MRI slap to a full FoV UNI scan of the same subject, but I get a false reorientation with my code (see attached image). I have tried multiple input and tried the script on different subjects. I also changed som flags such as -init-header and --cubic, but all seem to give the same results. bbregister --s MRS_200_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat --t2 --init-fsl mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_acpc_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_regt1.nii.gz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat –trilin I would appreciate to hear your thoughts on this problem. Have a nice weekend and kind regards, Jeltje Spapens

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Use pial or white surface area of FreeSurfer?
by free_learner 01 Jan '24

01 Jan '24

External Email - Use Caution Dear experts, Surface area is a commonly used metric. Unlike thickness and volume, area could be calculated based on white surface or pial surface in FreeSurfer. I don’t know which one should be better used for analysis. I believe the pial surface area is more sensitive to brain changes such as gray matter atrophy. But the white surface area is the default in FreeSurfer and thus probably the one used in papers. Maybe I should use the mean area of white and pial surface? Best, Yang Hu

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