Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

How to quickly check whether the segmentation of thalamic nuclei or the amygdala is correct
by 梁晓芳 22 Jul '21

22 Jul '21

External Email - Use Caution Hi, I have tried to segment the thalamic nuclei and amygdala, using segmentThalamicNuclei.sh and segmentHA_T1.sh. But is there any method to quickly check whether the segmentation is accurate? Because I have so many scans that using freeview to check the results one by one may cost me a lot of time. Meanwhile those volumes extracted from the segmentation are really important in my study. So I think I do need to ensure the accurate segmentation. Thank you very much! Best wishes, Xiaofang

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Brain size adjustments in FreeSurfer using Qdec
by Alejandro Meruelo 21 Jul '21

21 Jul '21

External Email - Use Caution Hello, Hope all is well! For cortical thickness statistical calculations in FreeSurfer using Qdec, is there any adjustment needed for brain size? Many thanks for your assistance, Alejandro

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Re: [Freesurfer] FreeView issue!
by fsbuild 21 Jul '21

21 Jul '21

External Email - Use Caution Your crash report listed an Intel Mac running BigSur 11.4.  The screenshot below shows running the freesurfer 7.2.0 release installed on an Intel Mac running BigSur 11.4 (after installing the pkg file from https://secure-web.cisco.com/1w0xxEMjJUzMzaNI7qL3KE_kI0NAwbdBtOto…)   In the terminal window you will see FS_LICENSE was manually set in the environment to point to the license.txt file.  But the environment variable QT_MAC_WANTS_LAYER is not in the environment at all.  After opening an empty freeview window, the volume /Applications/freesurfer/7.2.0/subjects/bert/mri/brain.mgz was loaded.  Please give that a try on your machine. - R.

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Control points and white matter segmentation
by Rosalia Dacosta Aguayo 21 Jul '21

21 Jul '21

External Email - Use Caution Dear Freesurfer team, Sorry for this basic question. I wonder if once I have edited the white matter (topological defects), I can run control points without deleting what I have done to white matter segmentation. Kind regards, Rosie

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delineating gyral boundaries in native space
by Robin Cash 21 Jul '21

21 Jul '21

External Email - Use Caution Hi, Is there a tool within freesurfer that can be used to delineate gyral boundaries (delineate sulci) from an individual's T1 scan in native space? To be clear, the purpose wouldn't be to broadly identify or parcellate different gyri, but to delineate the boundary between gyri and sulci. Many thanks, Robin Dr. Robin Cash (PhD) | ARC Senior Research Fellow Department of Biomedical Engineering, UNIVERSITY OF MELBOURNE Melbourne Neuropsychiatry Centre, Level 3, Alan Gilbert Building, 161 Barry St, Carlton VIC 3053 Australia Twitter<https://secure-web.cisco.com/1acjuoQqXB1dkDPlCJpMqGSMi53R45KVmVJko7Ik-Kfmqd…> | Google Scholar<https://secure-web.cisco.com/1Z4EkX_ch_GUS5nKc90QaGpU6mdLSm8Xs315eYJQOYKtpd…>

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sbTIV versus eTIV
by AJ 20 Jul '21

20 Jul '21

External Email - Use Caution Hi, I am looking at interscanner differences between Philip and GE. I get significantly less variation between the scanners when looking at sbTIV (coefficient of variation < 1.5 %) than eTIV (12%) within subjects. Any thought as to why? Normalizing ROIs with sbTIV improves these differences even more. Thanks for your help. AJ

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DOSS Question
by WON JONG CHWA 20 Jul '21

20 Jul '21

External Email - Use Caution Dear FreeSurfer Experts, I have been having trouble with performing DOSS analyses with mri_glmfit. One of the groups in my sample is too small to be performed with DODS, but when I try to call the DOSS option in mri_glmfit, it returns the same error, saying that DODS is not possible with this sample. I even tried defining the design matrix manually using --X, but it returns the same error. mri_glmfit --glmdir lh.rate.CI.paired-diff.thickness.DOSS --y mgh/rates/lh.thickness-rate.stack.fwhm10.mgh --fsgd FSGD/CI_baselines/paired-diff-demean-CI.fsgd doss --surf fsaverage lh --C Contrasts/BMICorrelationCI_DOSS.mtx gdfRead(): reading FSGD/CI_baselines/paired-diff-demean-CI.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 BMIatBaseline -1.49788e-08 3.57667 1 AgeAtFirstTP -5.62933e-08 3.40434 Class Size and Means of each Continuous Variable 1 MaleNormal 26 -0.5852 0.2393 2 MaleCI 2 0.8115 2.2778 3 FemaleNormal 38 0.2564 -0.2749 4 FemaleCI 6 0.6414 -0.0556 ERROR: Class MaleCI has 2 members. With 2 variables and using DODS, you need at least 3 members If anyone has any ideas on how to go about this, that would be greatly appreciated. Thank you. William

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Re: [Freesurfer] Developer password
by fsbuild 20 Jul '21

20 Jul '21

External Email - Use Caution I’ll send the info to your private email shortly. - R. On Jul 19, 2021, at 07:07, Clemens M <cmielach(a)mailbox.org> wrote:        External Email - Use Caution        Dear Freesurfer Team,I am currently setting up freesurfer using the Ubuntu VM but I can't log in because I don't have the developer password. Would it be possible to provide me with the password? Thank you!Best,Clemens_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Tenure research position in fMRI at ultra-high field, Neurospin, France
by Evelyn Eger 20 Jul '21

20 Jul '21

External Email - Use Caution Dear list members, A tenured researcher position for an MR scientist with focus on ultra-high-field fMRI is available at Neurospin (France’s advanced brain imaging center, located in the greater Paris area). The candidate should mainly help developing the applications of the center’s new 11.7 Tesla imaging system. Please see the attached job description for details on the ideal candidate’s profile. In case of interest, feel free to directly contact Nicolas Boulant (nicolas.boulant(a)cea.fr) with more specific questions. Thank you for your help in circulating this ad. Best regards, Evelyn Eger

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Announcing the new version of TRACULA, included in FreeSurfer 7.2
by Yendiki, Anastasia 20 Jul '21

20 Jul '21

Hi all - After a year of lockdown coding, and a couple more years of tireless work by the tract annotation team, we are pleased to share the new version of TRACULA. For a summary of new features see: https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Of note, new protocols were developed for the manual annotation of 42 tracts, which you can see here: https://dmri.mgh.harvard.edu/tract-atlas/ These tracts were manually annotated on the bmax=10000, 512-direction data from our Connectom scanner and we now use them as training data for TRACULA, allowing it to reconstruct the same tracts automatically in much lower quality (e.g., b=1000, 32- or 64-direction) data. More details in Chiara Maffei's preprint: https://www.biorxiv.org/content/10.1101/2021.06.28.450265<https://www.biorxiv.org/content/10.1101/2021.06.28.450265v2> The tutorials and documentation have been updated to reflect this new version: https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula I highly recommend skimming through the tutorial, even if you've used TRACULA in the past. A lot has changed in the configuration options, and there are some additional outputs that you can take advantage of. What we are missing is a new tutorial dataset that is compatible with this new version. That will have to wait until after our summer vacations 🙂 There is also ongoing work on adding more tracts, and more features to come in the future! In addition to Chiara and the tract annotation team (https://dmri.mgh.harvard.edu/tract-atlas/#acqknowledge) special thanks to Doug for his help integrating along-tract stats with the FreeSurfer statistical analysis tools, Ruopeng for the new visualization features for these along-tract stats in freeview, and Andrew for his patience with last-minute commit disasters... I hope everyone is having a great summer! Anastasia. | Anastasia Yendiki, Ph.D. | Associate Professor, Harvard Medical School | Associate Investigator, Massachusetts General Hospital | Martinos Center for Biomedical Imaging | 149 13th St. Suite 2301 | Charlestown, MA 02129 | Tel: 617-726-9434 | Fax: 617-726-7422 | Web: http://scholar.harvard.edu/a-y

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