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30081 discussions

Trying to highlight insula
by Kelli Ann Nini 25 Apr '21

25 Apr '21

External Email - Use Caution Greetings esteemed surfers, I am trying to take an image of the insula using the LUT. I've loaded volumes T1, wm, brainmask, and aseg respectively, and checked all three views but for some reason labels 19 and 55 (Left & Right Insula) "does not exist in volume". Thank you in advance! -Kelli NOTICE: This message, including all attachments transmitted with it, is intended solely for the use of the Addressee(s) and may contain information that is PRIVILEGED, CONFIDENTIAL, and/or EXEMPT FROM DISCLOSURE under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein is STRICTLY PROHIBITED. If you received this communication in error, please destroy all copies of the message, whether in electronic or hard copy format, as well as attachments and immediately contact the sender by replying to this email or contact the sender at the telephone numbers listed above. Thank you!

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asegstats2table: Cannot find stats file
by Haneen Hakeem 25 Apr '21

25 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I’m attempting to output stat files using “asegstats2table” and “aparcstats2table” but for some of my subjects I get the following error when I run the commands: ERROR: Cannot find stats file /apps/freesurfer/7.0.0/freesurfer/subjects/APC011/stats/aseg.stats However, when I check the stats file in FreeSurfer output directory, the stats files are there (including asset.stats). This issue is recurring with all “asegstats2table” and “aparcstats2table” stat files. 1) freesurfer version FreeSurfer 7.0 2) Platform: Bash remotely through High Performance Computing (HPC) on a MacOS Mojave 3) recon all log attached

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mri_glmfit FIR model
by Marilena Wilding 25 Apr '21

25 Apr '21

External Email - Use Caution Dear Freesurfers, I’m currently doing 2nd level analysis on a FIR model. I first concatenated my data with this command: isxconcat-sess -sf sessidlist -analysis FIR_group.lh -contrast global-v-local -no-hrf -hemi lh -o group_analysis I got 29 timepoints and their corresponding 29 ces.nii and cesvar.nii files. Then I ran glmfit (for each timepoint): mri_glmfit \ --y ces.000.nii \ --wls cesvar.000.nii.gz \ --surface fsaverage lh \ --glmdir group_GLM_lh_000.wls \ --osgm \ --nii.gz In my paradigm I’m showing a stimulus that can be seen in two ways. In my analysis I separate the runs, depending on what the participant indicated to have seen (1 or 2) and compute the contrast in activation between these two percepts. I was now wondering if the command above is correct with the ‘osgm’-flag? Since I’m only interested in the difference between the two conditions from the paradigm and not different groups of participants (e.g. patients vs. healthy people) I don’t have to specify a fsgd file, correct? And if I wanted to specify covariates I’d just make such a file but without groups and only variables? Thank you very much for your help! Best, Mara

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mri_convert error for creating flat_lh.gii file
by Suzanne Nie 25 Apr '21

25 Apr '21

External Email - Use Caution Hello Freesurfer Developers, I'm attempting to create a full surfaces folder in the filestore based on the example, with flat_lh.gii, inflated_lh.gii, pia_lh.gii, wm_lh.gii, and those for the right hemisphere in order to use cortex.quickshow, plt.show, and cortex.webgl.show. I used cortex.freesurfer.flatten to create files lh.full.flat.patch.3d and rh.full.flat.patch.3d from lh.full.patch.3d that I created from making cuts. I want to convert these files to flat_lh.gii, but mris_conver gives me segmentation fault errors. mris_convert lh.full.flat.patch.3d flat_lh.gii ASSERTION FAILED: /Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:4323 mris->dist_nsize == 0 ASSERTION FAILED: /Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:4323 mris->dist_nsize == 0 Segmentation fault: 11 I was unable to find similar issues. If my goal is to display using cortex.webgl.show, is creating these files the correct step and if so, are there any instructions explaining possible steps? - Freesurfer Version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 - Platform: macOS Catalina Version 10.15.7 - Darwin Suzannes-MBP 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64 - recon-all.log attached Thank you, Suzanne

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Hipppocampal segmentation on freesurfer
by Jindal, Saurabh 25 Apr '21

25 Apr '21

External Email - Use Caution Hi experts, I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that there is some non-hippocampal inclusion in the form of choroid plexus and adjacent peri-ventricular white matter. Do we have a standard cutoff criterion for hippocampal inclusion? Like how many voxels for how many slices is okay to let it pass? Saurabh ________________________________ 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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Hippocampus segmentHA_T1.sh
by Wei Shao 23 Apr '21

23 Apr '21

External Email - Use Caution Hello, Dear FreeSurfer expert I tried to use segmentHA_T1.sh for the hippocampus subfields, However, here is the log cannot find the wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all? But the wmparc.mgz and norm.mgz are there [image: Capture.PNG] Could you tell me how to fix this? Thanks! Best, Wei

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Question about volume matrix in hippocampus
by Wei Shao 22 Apr '21

22 Apr '21

External Email - Use Caution Hi, Freesurfer experts. I have used "quantifyHAsubregions.sh hippoSf" to gather the volume information from the hippocampus. A quick question about the volume matrix, would you tell me which label system ("HBT" "FS60" or "CA") this code used to extract the volume information? or there is no difference? Thanks Best, Wei

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Hippocampal Subfields
by Jindal, Saurabh 22 Apr '21

22 Apr '21

External Email - Use Caution Hi experts, I am focusing on hippocampus for my work using subfield analysis on freesurfer 7.1. Is there is way to run the container only for subfields or do we have to run recon_all on the subject first always? Thanks. Saurabh Postdoc Research Fellow ________________________________ 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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Postdoctoral Researcher Position in Adolescent and Infant Neuroimaging
by Jeffrey Spielberg 21 Apr '21

21 Apr '21

External Email - Use Caution *Attachment and Biobehavioral Catch-up Lab* *University of Delaware, Newark, DE* *Postdoctoral Researcher Position in Adolescent and Infant Neuroimaging* We invite applications for a postdoctoral position within a highly interdisciplinary lab at the University of Delaware investigating the short- and long-term effects of an evidence-based parenting program on brain development. The researcher will play a role in analyzing and publishing data from our NIH-funded randomized clinical trial that uses functional and structural MRI to investigate how enhanced early care shapes the developing connectome. The researcher will join an inter-disciplinary group of researchers with expertise in intervention science, genetics, psychophysiology (autonomic nervous system regulation and cortisol regulation) and neuroimaging (EEG and MRI). The candidate will be supervised by Dr. Mary Dozier, Dr. Nim Tottenham and Dr. Jeffrey Spielberg. REQUIREMENTS: - Ph.D. in neuroscience, psychology, clinical or developmental science or related disciplines - Experience processing and analyzing structural and functional MRI data ADDITIONAL HIGHLY DESIRED QUALIFICATIONS: - Proficiency in MATLAB or R and/or computer programming (e.g., bash scripting) - Previous publications using MRI data - Interest in neuroimaging of infants and adolescents - Strong interpersonal skills - Collaborative team member EXPECTED RESPONSIBILITIES: - Analyze human MRI data using various software tools (in particular FSL, Freesurfer) - Prepare manuscripts for publication - Collaborate with graduate students and assist in their training in data processing and analysis - Assist with data collection and organization of participant data - Participate in grant and laboratory management How to apply: Please email your CV, a brief statement of research experience and interests, and a list of three references with contact information to Dr. Mary Dozier (mdozier(a)udel.edu) For more information on the lab’s work, see: http://secure-web.cisco.com/1SxgDGinFmIeQuPoN8yeUtMVtl17FMqlcTwlK7zPrVkLAYP… -- Jeffrey M. Spielberg, Ph.D. Assistant Professor, Clinical Science Department of Psychological and Brain Sciences University of Delaware Newark, DE 19716 Lab: Suite 405 Wolf Hall Email: jmsp(a)udel.edu Website: http://secure-web.cisco.com/17lxMc4SBgA-riBFZdmUtiIpQotTNwUrJVED9Lk8uLUOtrg…

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mri_recon-all error : number of vertices does not match surface
by 林鈺庭 21 Apr '21

21 Apr '21

External Email - Use Caution Dear FreeSurfer Developers: We analyzed MRI T1 image data on freesurfer and encountered some difficulty, could you help us with this? The recon-all.log file is already attached in this email in case you need it. We thank you in advance. - FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - program versions used:$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ Best regards, Josephine

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