Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Re: [Freesurfer] TRACULA FS 7.2.0 Error: domainname: Command not found. Too many )'s.
by fsbuild 23 Jul '21

23 Jul '21

External Email - Use Caution Hello Jürgen, /bin/domainname should be installed as part of the base distribution on a linux machine.  Maybe it was not in your PATH before you ran the freesurfer shell setup script?   You could test this by starting with a basic PATH, e.g., on CentOS, $ export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin$ which domainname/usr/bin/domainname … then add in anything else to PATH  … $ source $FREESURFER_HOME/SetUpFreeSurfer.sh … output deleted … $ which domainname/usr/bin/domainname - R. On Jul 23, 2021, at 01:50, juergen.haenggi(a)upd.unibe.ch wrote:domainname: Command not found.

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TRACULA FS 7.2.0 Error: domainname: Command not found. Too many )'s.
by juergen.haenggi＠upd.unibe.ch 23 Jul '21

23 Jul '21

External Email - Use Caution Dear TRACULA experts I am trying to run the new version of TRACULA implemented in FS 7.2.0 on a Mac and the following error occurred at the beginning of trac-all -prep: trac-all -prep -c /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/tracula_config_IPS_all_example_DICOMs_FS720.txt domainname: Command not found. Too many )'s. ERROR: Syntax error in configuration file /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/tracula_config_IPS_all_example_DICOMs_FS720.txt I checked the configuration file with respect to the brackets, but did not find too many )’s. What does it mean "domainname: Command not found.“ and could it be that this error is related to "Too many )’s."? The config file is attached and no log file is produced. Any advise is greatly appreciated Thanks in advance Regards Jürgen

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Re: [Freesurfer] [EXT] Freesurfer Digest, Vol 209, Issue 33
by Robin Cash 22 Jul '21

22 Jul '21

External Email - Use Caution Many thanks for this quick response! ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Thursday, July 22, 2021 1:22 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXT] Freesurfer Digest, Vol 209, Issue 33 External email: Please exercise caution Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1ZN-z9XulKsgjGsnuVq9RYfciZ9kZkjstwRZmKIIZmwnLo… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Developer password (Eli Bulger) 2. Re: dwi_orig_las issue trac-all -prep (AmirHussein Abdolalizadeh) 3. DOSS Question (WON JONG CHWA) 4. Re: dwi_orig_las issue trac-all -prep (Yendiki, Anastasia) 5. sbTIV versus eTIV (AJ) 6. Re: sbTIV versus eTIV (Douglas N. Greve) 7. Re: sbTIV versus eTIV (AJ) 8. Total WM surface area (Alexopoulos, Dimitrios) 9. Intensity equalization (AJ) 10. delineating gyral boundaries in native space (Robin Cash) 11. Re: dwi_orig_las issue trac-all -prep (AmirHussein Abdolalizadeh) 12. Control points and white matter segmentation (Rosalia Dacosta Aguayo) 13. Re: dwi_orig_las issue trac-all -prep (Yendiki, Anastasia) 14. Re: Intensity equalization (Fischl, Bruce) 15. Re: delineating gyral boundaries in native space (Fischl, Bruce) 16. Re: Control points and white matter segmentation (Fischl, Bruce) 17. Re: Control points and white matter segmentation (Rosalia Dacosta Aguayo) 18. shortest distance between two points along the gray/white boundary (Krieger, Donald N.) 19. Re: Control points and white matter segmentation (Fischl, Bruce) 20. Re: shortest distance between two points along the gray/white boundary (Fischl, Bruce) 21. Re: (no subject) (Stephanie K) 22. Re: shortest distance between two points along the gray/white boundary (Krieger, Donald N.) ---------------------------------------------------------------------- Message: 1 Date: Tue, 20 Jul 2021 18:06:31 +0000 From: Eli Bulger <esbulger(a)cmu.edu> Subject: Re: [Freesurfer] Developer password To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <6451b1940990455c966dacc981f091a9(a)cmu.edu> Content-Type: text/plain; charset="windows-1252" External Email - Use Caution Hello, I am also in need of the developer password for running freesurfer through VirtualBox. Is it possible to get the info sent to my email? Thank you, Eli ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of fsbuild <fsbuild(a)contbay.com> Sent: Monday, July 19, 2021 1:26:29 PM To: freesurfer(a)nmr.mgh.harvard.edu Cc: cmielach(a)mailbox.org Subject: Re: [Freesurfer] Developer password 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 list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1MK_eM4w5iLJoVfKdbMztBDiSsJ6hNdFRReC2Mr9YN-i3v…<https://secure-web.cisco.com/15Z7A9Lammwjhl7fkK9gwCVHnnXsseRlOHwcILJVS3QpOG…>

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Freeview question
by Nasiriavanaki, Zahra,M.D. 22 Jul '21

22 Jul '21

Hello experts, I am trying to load two types of labels on left hemisphere of a single subject. In tksurfer, both labels load without an issue, but in Freeview, one type of labels (neg.label) don’t show up. There is no error in the terminal, so I’m not sure what’s going on. I copied the labels and subject’s lh.inflated in the scratch directory below: /autofs/cluster/scratch/thursday/mona I need to use Freeview, since I’ve written a code to take screen shots. Deeply appreciate it if you could please help me on this. Thanks, Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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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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