Freesurfer July 2021

freesurfer@nmr.mgh.harvard.edu

91 participants
121 discussions

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

2 2

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.

3 3

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

2 3

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…>

2 1

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

2 2

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

1 0

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

2 1

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

1 0

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

1 0

Re: [Freesurfer] Announcing FreeSurfer version 7.2
by fsbuild 20 Jul '21

20 Jul '21

External Email - Use Caution While it does not currently work to change the default install path, that default install path for the .deb (and .rpm) 7.2.0 installer files is /usr/local/freesurfer/7.2.0 (which reads like the path you want to use). If you already have different releases under /usr/local/freesurfer/<rev> that are not rev=7.2.0, e.g. from using the tar files (as this is the first .deb package), then the packaging tools won’t know anything about them and should not touch them when installing 7.2.0.  Or apt install and apt remove will only affect /usr/local/freesurfer/7.2.0 with the freesurfer_7.2.0_amd64.deb package. Still looking into nu_correct. - R. On Jul 20, 2021, at 06:21, Kiyotaka Nemoto <kiyotaka(a)nemotos.net> wrote:        External Email - Use Caution        Hello R,Thank you for letting me know that the deb file is now available. It's so useful for Ubuntu users to install FreeSurfer using the deb file.Can I ask you one more question? Can I specify the install directory using the deb file?I manage different versions of FreeSurfer by installing under /usr/local/freesurfer/{6.0.1, 7.1.1, 7.1.2}.If I can specify the directory, then I would love to use the deb file.As for the missing mni directory, I'm concerned about nu_correct.In my understanding, recon-all still uses nu_correct as default unless we set DoAntsN3 or DoAntsN4.nu_correct is located under $FREESURFER_HOME/mni/bin, so I thought it might be missed for some reason.Best regards,KiyotakaOn Tue, Jul 20, 2021 at 3:32 PM fsbuild <fsbuild(a)contbay.com> wrote:Hello Kiyotaka,You may not need to be concerned about that warning.  You can suppress it by setting the following in your shell environment.$ export NO_MINC=1For Ubuntu linux, if you have sudo/root/admin privileges, then you could try running the installer file instead of using the tar file, i.e.,$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb- R.On Jul 19, 2021, at 21:08, Kiyotaka Nemoto <kiyotaka(a)nemotos.net> wrote:        External Email - Use Caution        Dear Doug,Thank you for the announcement of 7.2.0 update.I updated using freesurfer-linux-ubuntu18_amd64.tar.gz and noticed that the 'mni' directory is missing.As a result, now the shell shows warning about MNI=====-------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/username/freesurfer/7.2.0/subjectsWARNING: MINC_BIN_DIR not defined.         'nu_correct' and other MINC tools         are used by some Freesurfer utilities.         Set NO_MINC to suppress this warning.WARNING: MINC_LIB_DIR not defined.         Some Freesurfer utilities rely on the         MINC toolkit libraries.         Set NO_MINC to suppress this warning.FSL_DIR           /usr/local/fsl=====Is it intended?Best regards,KiyotakaOn Tue, Jul 20, 2021 at 7:45 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:We are  please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check outMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1BlHjRo1wiRb2WvddH8GfD4hFYtxGnnXI7YbPO… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web..cisco.com" claiming to be https://secure-web.cisco.com/1z6kK1yL1k60FJGc27E2kn8x07SbszbMudIGBC… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1O14LpmCbLrvsH2LqoMBFq1uWO82zk5EdVR0-If…;. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. -- Kiyotaka Nemoto, M.D., Ph.D.Associate ProfessorDepartment of PsychiatryDivision of Clinical Medicine, Faculty of MedicineUniversity of Tsukuba1-1-1Tennodai Tsukuba, Ibaraki 305-8575, JapanE-mail: kiyotaka@nemotos.net_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

← Newer
1
2
3
4
5
6
7
8
...
13
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer July 2021