Freesurfer August 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
152 discussions

problems with brainmask.mgz and wm.mgz files
by Dalton Bermudez 24 Aug '20

24 Aug '20

External Email - Use Caution For some reason when I ran the recon-all command it generated a brainmask.mgz file which excluded part of the right hemisphere and a wm.mgz which did a horrible job at segmenting gray matter from white matter. The recon-all command later exited with an error. How do I fix the problem? I have attached the recon-all.log file for your reference. Thank you, Dalton

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FreeSurfer6 hires patch for longitudinal output
by Nandita Vijayakumar 24 Aug '20

24 Aug '20

External Email - Use Caution Dear FreeSurfer team, I have processed my data through the longitudinal stream of FreeSurfer6 using the -hires flag. I would like to apply the patch to fix the global metrics, but seem to run into an error when supplying the longitudinal subject directory. I've tried running the following command: recon-all -long sub-001_wave1.long.sub-001 sub-001 -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels But get the following error: Unmatched ". The command seems to work fine on the cross-sectional directories. So I'm wondering if the patch can be applied to longitudinal directories? Thanks, Nandi

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Segmentation Labels for the Skull
by mudassar liaq 24 Aug '20

24 Aug '20

External Email - Use Caution Hi, (A but of a dumb question but) Is there any way we can also have skull also labeled () along with the brain parts in MRI output? [image: image.png] * Skull mentioned by white arrows Thanks and Regards,

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recon-all exited with error
by Dalton Bermudez 23 Aug '20

23 Aug '20

External Email - Use Caution ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1 size(0) = 1, 0.976562, 0.976562 error: No such file or directory error: MultiRegistration::loadMovables: voxel size is different /home/dbermudez/Documents/subjects/00_0001/mri/orig/002.mgz. However, I have checked the dimensions of both the T1w and the T2w and they both have the same dimensions: 176×256×256. I do not know what is the problem? and how can I fix the issue?

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FastSurfer with FreeSurfer version 7.1.0?
by Billah, Tashrif 22 Aug '20

22 Aug '20

Hi Barbara and Martin, I didn't have any problem running FastSurfer with FreeSurfer 7.1.0 either. Best, Tashrif

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ROI-wide cortical thickness for each network !
by Martin Juneja 22 Aug '20

22 Aug '20

External Email - Use Caution Hi experts, I extracted network-wise cortical measures (i.e., 7 cortical thickness values for 7 networks for Yeo atlas). I was wondering if there is a way to get the cortical thickness of each ROI within each of these networks e.g., cortical thickness values of all the ROIs which constitute default-mode network of Yeo's 7 network parcellation, and then cortical thickness values of all the ROIs which constitute limbic network of Yeo's 7 network parcellation, and so on. I know Desikan atlas can be used to get morphometry measures of 34 ROIs per hemisphere. But the problem is that e.g., default-mode ROIs from Desikan atlas do not completely overlap with the DMN of 7-network parcellation from Yeo atlas. In other words, superior frontal cortex from default-mode network of Yeo 7 network parcellation is a big chunk compared to several small ROIs (some partial and some full) in Desikan atlas, so I do not see any way how to find ROIs which just match with that superior frontal cortex of default-mode of Yeo's 7 network. Any help would be much appreciated !

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How to run recon-all for different subjects and each subject with different sessions ?
by Camargo, Aldo 21 Aug '20

21 Aug '20

External Email - Use Caution Hi Freesurfer experts, I have a question: How to run recon-all for different subjects and each subject with different sessions ? Thanks a lot in advance and have a nice day, Aldo

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extracting beta coefficients and p-values
by Rizvi, Batool 21 Aug '20

21 Aug '20

External Email - Use Caution Dear FreeSurfer experts, After running the longitudinal pipeline with QDEC, I needed beta-values of the associations between my main continuous variable and the significant cortical cluster, as well as of all the nuisance factors/categorical variables. Since the summary file doesn't list beta values, I attempted running this command to find beta coefficients: mri_segstats --i beta.mgh --annot fsaverage lh lh-Avg-long.thickness-spc-Parietal_WMH-Cor/mc-z.abs.th20.sig.ocn.annot --excludeid 0 --avgwf avgwf.dat >From this, I got this output file listing beta values for 1 cluster (entorhinal cortex) that was related to my main continuous IV (parietal WMH). I'm struggling to understand how to still compute 1 beta-coefficient per variable from this list. I understand that this list, based on my fsgd file, can be split into 4 sets of numbers, but I'm not sure what do next. avgwf.dat: 0.93879 -8.80748 0.38452 3.13252 -0.09493 -0.13107 -0.09960 -0.31087 -0.02291 0.03127 -0.02417 -0.07858 0.13087 1.80749 0.32535 0.64947 Below is how my fsgd file was structured: GroupDescriptorFile 1 Title ParietalWMH_age_gender_APOe_EC_left MeasurementName long.thickness-spc Class APOE_statusNO-genderF Class APOE_statusYES-genderF Class APOE_statusNO-genderM Class APOE_statusYES-genderM Variables Parietal_WMH age_years Avg_ECthickness Input W38284_base APOE_statusNO-genderF 0.732010 85.830000 3.125000 .. (only listing the 1st Input line here) My contrast file (C.dat) looks like below: 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 So basically, I would like to get beta coefficients for the below variables: * Parietal WMH * Age * Gender * APOE status * Average EC thickness (baseline values) Thank you so much in advance for your help! Batool

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Postdoctoral scientist positions at UCSF
by Tosun, Duygu 21 Aug '20

21 Aug '20

External Email - Use Caution We are seeking highly talented and self-motivated postdoctoral scientists with experience in quantitative medical imaging and biomarker research. The research will be conducted at the University of California San Francisco (UCSF) and San Francisco Veterans Affair Medical Center. The successful candidate will interact with multidisciplinary project teams focused on identifying and characterizing neuronal substrates of cognitive and clinical decline and optimizing and streamlining biomarker discovery in neurodegenerative diseases and psychiatric disorders. Qualified candidate will have Ph.D. with practical experience in medical imaging, fluid biomarkers, and neurobiology along with a solid understanding of biostatistics. Training or experience in the areas of neuroinformatics, computational neuroscience, and machine learning is preferred. Candidate is expected to learn new techniques as necessary. The successful candidate will have demonstrated a track record of success as evidenced by relevant publications in leading peer-reviewed journals. Candidate must demonstrate outstanding communication skills, the ability to operate within multidisciplinary environments, creativity, and a high degree of intellectual independence. Attention to detail and enthusiasm for science are a must. This postdoctoral research fellowship program is designed to prepare the fellow for independent academic career in reproductive research. Focus will be scientific productivity demonstrated by innovative research, publication in high impact journals and successful extramural funding. Fellow is expected to transition in few years into an independent faculty role. Applications will be accepted until the positions are filled. Funding is available for the selected applicants to start immediately. When electronically applying for this position (duygu.tosun(a)ucsf.edu) please include (in one PDF document) a cover letter, curriculum vitae, publication list and a brief description of research interests. Duygu Tosun-Turgut, PhD Director, Medical Imaging Informatics + Artificial Intelligence Associate Professor, UCSF Department of Radiology and Biomedical Imaging https://profiles.ucsf.edu/duygu.tosun-turgut <https://profiles.ucsf.edu/duygu.tosun-turgut> University of California, San Francisco Center for Imaging of Neurodegenerative Diseases (CIND) 4150 Clement Street - 114M San Francisco, CA 94121 Phone: (415) 221-4810 ext. 23650 duygu.tosun(a)ucsf.edu

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Generating Global Thickness and Surface Area Estiamtes from .aparc variables
by Plotkin, Micah 21 Aug '20

21 Aug '20

External Email - Use Caution Dear Freesurfer Experts, I want to generate global measures of cortical thickness and pial surface area analogous to using total cerebral volume as a global brain volume estimate. In your opinion, would it be reasonable to generate these global thickness and surface area estimates from the following .aparc variables: SurfArea.lh.Frontal MeanThick.lh.Frontal SurfArea.rh.Frontal MeanThick.rh.Frontal SurfArea.lh.Occipital MeanThick.lh.Occipital SurfArea.rh.Occipital MeanThick.rh.Occipital SurfArea.lh.Parietal MeanThick.lh.Parietal SurfArea.rh.Parietal MeanThick.rh.Parietal SurfArea.lh.Temporal MeanThick.lh.Temporal SurfArea.rh.Temporal MeanThick.rh.Temporal Regards, Micah ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Freesurfer August 2020