Freesurfer July 2021

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91 participants
121 discussions

Fwd: TRACULA FS 7.2.0 Error: domainname: Command not found. Too many )'s.
by juergen.haenggi＠upd.unibe.ch 26 Jul '21

26 Jul '21

External Email - Use Caution Dear R, dear Anastasia thanks for your answer. there is indeed no domainname command in /usr/bin. I am working on a Mac and I am wondering why this error did not occur if using TRACULA in FS 7.1.1 if this command is not available on my Mac. please can you explain in more detail how I can fix this problem on a Mac if using tcsh? Thanks in advance Regards Jürgen Am 23.07.2021 um 08:17 schrieb fsbuild <fsbuild(a)contbay.com<mailto:fsbuild@contbay.com>>: 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<mailto:juergen.haenggi@upd.unibe.ch> wrote: domainname: Command not foundDear 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] dwi_orig_las issue trac-all -prep
by AmirHussein Abdolalizadeh 25 Jul '21

25 Jul '21

External Email - Use Caution Hi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using?

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Tracula on a stand alone workstation
by Alan Francis 24 Jul '21

24 Jul '21

External Email - Use Caution Hi Anastasia - Is it possible to run Tracula on a stand alone Linux machine (Ubuntu) which has 64 GB RAM and hyper threading? At Martinos, I used to run this on the cluster. Thanks, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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Running local lGI for longitudinal subject gives error: Unmatchted "'"
by Tim Schäfer 23 Jul '21

23 Jul '21

External Email - Use Caution Dear FreeSurfer experts, I am trying to compute local lGI in FreeSurfer 6 for a subject that has undergone longitudinal processing. In this example, the longitudinal base subject folder (with the long template recon-all output for that subject) is called "111002" and the folder with the data for timepoint 1, for which I would like to compute lGI now, is called "111002_MR1.long.111002". So I run the following command: recon-all -long 111002_MR1.long.111002 111002 -localGI The only output, after less than a second, is: Unmatched '"'. Then the script terminates and I am back at the shell. Any thoughts on this or ideas? I have successfully computed local lGI for the cross subjects on the same computer, it finished this morning (using the command 'recon-all -s $CROSS_SUBJECT -localGI'). So the recon-all command in general seems to work, the error is specific to the lgi long command it seems. Here is some system info: > cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > uname -a Linux lxsrv2 5.8.0-59-generic #66~20.04.1-Ubuntu SMP Thu Jun 17 11:14:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux All the best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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shortest distance between two points along the gray/white boundary
by Krieger, Donald N. 23 Jul '21

23 Jul '21

External Email - Use Caution Dear experts, I would like to compute the shortest distance along the gray/white boundary between two points on the boundary, i.e. between points with "white" parcellation regions. The distance need not be guaranteed to be minimized and the path need not be unique. Can you suggest an approach using the freesurfer tools? Thanks - Don Department of Neurological Surgery University of Pittsburgh

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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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Freesurfer July 2021