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30086 discussions

Longitudinal Hippocampal Subfields - negative subfield volume values
by Ashwati Vipin (NNI) 03 Jul '20

03 Jul '20

External Email - Use Caution Dear FreeSurfer Developers, I've run the longitudinal hippocampal subfield pipeline using the following command on freesurfer version 6.0: longHippoSubfieldsT1.sh PAWS001_base_FS I received no errors and everything seems to have run fine. But on computing the subfields using the following command: quantifyHippocampalSubfields.sh T1.long PAWS_longitudinalhipsubfields.txt I noticed that all of subfields have negative volume values. I checked the individual text files within each subject's timepoint and indeed the output is showing negative volumes as shown below: [Inline image OWAPstImg380689] I have also tested the same subject and run the cross-sectional hippocampal subfield pipeline using the following command: recon-all -s PAWS001_TP1_FS -hippocampal-subfields-T1 I received the following output with volumes: [Inline image OWAPstImg750361] I'm really not sure why the longitudinal pipeline is showing negative values. Could it be a Freesurfer version issue? Am I doing something wrong? It is especially mind-boggling since I receive no error and the command is running smoothly! Please help. Thank you so much!! Best regards, Ashwati [cid:image42562a.PNG@52924320.49ad9bd1] nnitagl1

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Cerebellum segmentation
by Álvaro Deleglise 03 Jul '20

03 Jul '20

External Email - Use Caution Hi! I was wondering how can I run a segmentation of the cerebellum with a different strategy than the one provided by the default subcortical segmentation (which only differentiates lh and rh white and grey matter). I'm currently analyzing longitudinal data from a motor learning experiment in which the cerebellum it's very important, so I would like to have more cerebellar ROIs. I recently found an article by Makris et al., 2003, *Human Cerebellum- Surface-Assisted Cortical Parcellation and Volumetry with Magnetic Resonance Imaging,* but I'm not sure if there is any implementation of this strategy. Does anyone knows how can I use it? Or if there is another segmentation strategies available? *Thanks in advance.* * Álvaro Deleglise *

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Re: [Freesurfer] Subfield parcellation in 1.5 T and 2.6 mm Thickness
by Iglesias Gonzalez, Juan E. 02 Jul '20

02 Jul '20

Dear Victor, Sorry for the slow response. 1.5 T is not a problem. Do you have a companion 1mm T1? If no: then the main problem is the main recon stream. If yes: what is the in-plane resolution and orientation? If it’s a high-res coronal, it may help with the subfields. For the thalamus, I’d just use the 1 mm T1. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" <vzeng(a)bidmc.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, June 25, 2020 at 17:56 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Cc: "joliehoang22(a)gmail.com" <joliehoang22(a)gmail.com> Subject: [Freesurfer] Subfield parcellation in 1.5 T and 2.6 mm Thickness Hi FS developers, We were wondering whether a MRI scan that has 2.6 mm thickness + is 1.5 T would be sufficient for a subfield analysis (amygdala, hippocampus, thalamus). Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ 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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Fw: Hard Error Troubleshooting
by McManus, Peter 02 Jul '20

02 Jul '20

?Hello, I'm emailing for assistance regarding 6 hard-failed FS subjects (out of 1000) that were re-processed and still prematurely terminated at different pre-processing stages (using FS 7.1). The job was completed on a SLURM computing cluster affiliated with Boston Children's Hospital's E2 server, and I've attached the recon-all.logs for clarity, although none of the logs report an "exit with errors" but rather simply stop running. Do you have any idea what the issue(s) might be? Hopefully this is enough information to work with, as I'm not the one who actually ran the commands and am a new RA trying to get acclimated to the computational environment at BCH. Thanks for the help. Best, Peter

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Recon-all 5.3.0 failing and I can't see the error message
by Ian 02 Jul '20

02 Jul '20

External Email - Use Caution I have attached the log - is there any chance you could tell me what the problem is? Thanks, Ian --

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Re: [Freesurfer] How can I create a grey matter volume in Matlab?
by Franziska Klein 02 Jul '20

02 Jul '20

External Email - Use Caution Hello again, unfortunately, nobody is responding. . Until now I am able to create meshes from the freesurfer output files with the isosurface() and read_surf() functions from a MATLAB based toolbox . However, I still do not know with which combinations of the outputs of recon-all I could create a grey matter only mask. My goal is to get subject specific channel MNI coordinates projected onto the cortex (grey matter). My solution at the moment is to simply use the pial surfaces (rh.pial and lh.pial), however, I am not sure if this is sufficient. Any thoughts or ideas maybe? Thanks, Franziska ________________________________ Von: Franziska Klein Gesendet: Mittwoch, 27. Mai 2020 11:05 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: How can I create a grey matter volume in Matlab? Dear freesurfer user, due to the Covid 19 situation I am working in home office with a windows computer and can not run any freesurfer functions (installing a virtual box is not really an option). For all my subjects I do already have all output files from recon all. In the output, I found a wm.mgz but unfortunately there is no gm.mgz. Is it somehow possible to create a grey matter volume by using the recon all output in combination with Matlab? Thank you and kind regards, Franziska ------------------------------------------ Franziska Klein, M.Sc. Neurocognition and Functional Neurorehabilitation Group Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-066 Phone: +49-441-798-4947 Fax: +49-441-798-5522

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Bounding box dimensions for mri_cvs_register (MNI space)
by Elizabeth Haris 02 Jul '20

02 Jul '20

External Email - Use Caution Hi guys, I have a couple of queries regarding the output dimensions for mri_cvs_register. 1. If I am registering my images to MNI space, can the command give me a 2mm image, or will I only get a 1mm image which I then need to convert into a 2mm? I am currently getting a 1mm image and resampling it to a 2mm image afterwards (for fMRI analysis), using the following commands, and wanted to double check the procedure: * CVS command: mri_cvs_register --mov <subjID> --mni * FSL command: flirt -in <final_CVSmorphed_tocvs_avg35_inMNI152_norm.nii> \ -ref < final_CVSmorphed_tocvs_avg35_inMNI152_norm.nii > -applyisoxfm 2.0 -nosearch \ -out <subject_MNI_2mm.nii> 1. I also noticed that when I resample the image this way, though its dimensions are 2mm^3 the voxels in the bounding box are different to the voxels in my 2mm^3 functional image preprocessed in FSL (FS: 128^3 vs FSL: 109 91 109). * Is this a problem? * If so, is there a way to rectify this? Many thanks! Liz

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Longitudinal pipeline in pediatric sample with TIV difference
by Jose Pariente 02 Jul '20

02 Jul '20

External Email - Use Caution Hello Freesurfers experts, I have a pediatric sample and I wanted to use the longitudinal pipeline (the time acquisitions are 8 years apart and age range is from 6 years to 17). I saw that longitudinal pipeline assumes that TIV doesn't change, which in my sample is not true, but in Forums I saw that it can be done if you check that the average template and the images are well segmented. Is there something that can help me to determine this? For instance, a certain difference in eTIV between post and pre acquisition? Thanks, Jose Pariente

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Two research assistant positions
by Osher, David E. 01 Jul '20

01 Jul '20

External Email - Use Caution RESEARCH ASSISTANT We are recruiting 2 technical research assistants in the Cognition and Brain Circuitry Laboratory of Dr. David Osher at the Ohio State University. Primary duties for both positions include: conducting neuroscience research on the functional and structural architecture of the human brain, and its role in cognition; programming, running, and analyzing behavioral and brain-imaging experiments using functional magnetic resonance imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and behavioral assessments; scoring and coding data; performing statistical analyses using programs such as, MATLAB, Python, and shell scripting; recruiting research participants; maintaining participant databases; developing outreach letters. Positions are available for one year with the possibility of extension based on satisfactory performance and availability of funds. Required qualifications include: Bachelor's degree in psychology, neuroscience, cognitive science, computer science, data science, engineering, physics, or math; conduct of social science research is required; experience in a social science research capacity. Highly desired: strong mathematical, statistical, and coding skills (e.g., MATLAB, Python, shell scripting); strong interpersonal skills for interacting with a diverse group of people; strong organizational skills. This position is an excellent opportunity for individuals considering future graduate studies in cognitive and computational neuroscience. We are seeking an aspiring, self-motivated researcher with strong coding/programming skills who is excited about the brain, cognitive neuroscience, and/or clinical disorders and demonstrates evidence of a serious interest in a career in the field. If you are interested in being considered for these positions, please apply online at https://www.jobsatosu.com, under job listing #459935 (100%) and/or #459934 (75%) and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. David Osher at osher.6(a)osu.edu<mailto:osher.6@osu.edu> The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status.

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POSTDOC POSITION - modeling the functional and structural architecture of the visual system
by Osher, David E. 01 Jul '20

01 Jul '20

External Email - Use Caution POSTDOCTORAL SCHOLAR We are recruiting a Post Doctoral Scholar in the Cognition and Brain Circuitry Laboratory of Dr. David Osher at the Ohio State University. The Post Doctoral Scholar will plan, design, and conduct research using computational models to investigate the functional and structural architecture of the brain. This position is available for one year with the possibility of extension based on satisfactory performance and availability of funds. Required qualifications include Ph.D. in cognitive neuroscience, psychology, or related field; research experience in neuroimaging methods (magnetic resonance imaging (MRI), functional magnetic resonance imaging (fMRI), diffusion-weighted (DWI,) and/or functional connectivity). Desired qualifications include proficiency in coding; interest in any or all of the following: understanding the functional and structural architecture of the brain, computational modeling of individual differences in brain and behavior (especially in attention and perception), training and neural plasticity, and computational models of the human visual system. If you are interested in being considered for this position, please apply online at https://www.jobsatosu.com, under job listing #459936 and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. David Osher at osher.6(a)osu.edu<mailto:osher.6@osu.edu> OSU is located in Columbus, Ohio and is home to a vibrant community of cognitive neuroscientists, computational modelers, and vision scientists in the Psychology Department and Center for Cognitive and Brain Sciences. Postdocs will have access to state-of-the-art MRI and EEG facilities located inside the Psychology building. The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status.

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