Re: [Freesurfer] FW: Freeview Application

[zkaufman]

Recently Microsoft announced bash on Windows and initial tests within our
group have shown that freesurfer and freeview work in this environment:

  https://msdn.microsoft.com/en-us/commandline/wsl/about

However, currently freeview is not shipped as a separate stand-alone
package from freesurfer. However, this could probably be done with a small
amount of effort. If this is something of general interest perhaps I can
add this stand-alone package to the Download page.

-Zeke

> Just wanted to re-circulate this.
> Thanks in advance!
>
> Panos
>
> Panagiotis Fotiadis
> Research Technologist II
> J. P. Kistler Stroke Research Center
> Massachusetts General Hospital
> 175 Cambridge Street, Suite 300
> Boston, MA, 02114
> T: (617) 643-3869
> 
> From: Fotiadis, Panagiotis
> Sent: Monday, June 05, 2017 1:14 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Freeview Application
>
> Hello FS team,
>
> Is there any way to download FreeView as a standalone application on a
> Windows computer, or would I need to download freesurfer as a whole and
> then VPN?
>
> Thanks in advance!
> Panos
>
> Panagiotis Fotiadis
> Research Technologist II
> J. P. Kistler Stroke Research Center
> Massachusetts General Hospital
> 175 Cambridge Street, Suite 300
> Boston, MA, 02114
> T: (617) 643-3869
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Error in Reconstruction of bert samples.

[zkaufman]

Thats odd. Does that file exist? What are the permissions of it?

  ls -l
/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz




> IPL Neurosurgery has shared a OneDrive file with you. To view it,
> click the link below.
>
>
> 
> [https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]
>
> recon-all 1.log
>
>
>
>
> Hi,
>
>
> We have encountered a error in skull stripping process in bert sample. We
> are a novice. We attached the log.
>
>
> Command : recon-all -s bert -all
>
>
> #@# Skull Stripping Sat Mar 18 14:58:05 IST 2017
> /home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri
>
>  mri_watershed -rusage
> /home/iplneurosurgery/Documents/freesurfer/subjects/bert/touch/rusage.mri_watershed.dat
> -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas
> /home/iplneurosurgery/Documents/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca
> transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
>
>
> Keeping brain edits brainmask.auto.mgz brainmask.mgz
> Mode:  T1 normalized volume
> Mode:  Use the information of atlas (default parms, --help for
> details)
> mghRead(/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz,
> -1): read error
>
> *
> The input file is T1.mgz
> The output file is brainmask.auto.mgz
> No such file or directory
> Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18
> 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s bert exited with ERRORS at Sat Mar 18 14:58:06 IST 2017
>
> freesurfer version:
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>
>
> Platform: Cent OS 7
>
>
> uname -a : 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017
> x86_64 x86_64 x86_64 GNU/Linux
>
> Any Suggestion will be appreciated.
>
>
> Thanking you,
>
>
> IPL Neurosurgery.
>
>
>
> Sent from Outlook
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Re: [Freesurfer] freesurfer license tx

[zkaufman]

Usually it would be /usr/local/freesurfer

If thats what you did than you may need root access to the machine to be
able to do that. So basically create the license.txt file in your home
directory than copy it to the frresurfer folder:

  sudo cp license.txt /usr/local/freesurfer/

Bottom line is you need to put that license.txt file in the same location
that freesurfer was installed (Under the freesurfer folder).



>
>
> i received the license through the email and tried to make a new text file
> contains the emailed licensed details .. i am confused where exactly to
> save it
>
> i tried to save it in the user/local/freesurfer but it show a permission
> error
> "ou do not have the permissions necessary to save the file. Please check
> that you typed the location correctly and try again"
>
>
> i am using the newest freesurfer release and the Ubuntu 16.04 I'm
> completely new to Linux and
>
> thanx a lot
>
> fatima
>
> PhD student
>
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>
>
>

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Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

[zkaufman]

Hello Daniela,

Ive been looking into this error, and although I am unable to replicate it
on my Mac, I do have what might be a potential solution. Could you please
source freesurfer, then run the following command.

  $> sudo -E fs_update

Then retry the subject with the parallel flag. Please let me know how it
goes if you end up trying again. Thanks.

-Zeke

> I second the problem found in this thread:
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51917.html
>
> I recently downloaded FreeSurfer v. 6 on a macOS 10.12. To work around the
> System Integrity Protection issue, I installed my freesurfer folder in a
> local "Documents" folder instead of in Applications and that seemed to
> allow me to keep System Integrity Protection enabled while running
> FreeSurfer commands.
>
> Last night I ran recon-all on the same subject simultaneously, one using
> the -parallel tag and the other without it. This morning I see that only
> the one with the -parallel tag exited with errors and it seems to be this
> same "lazy symbol" error (see attached for recon-all error log).
>
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Users/Ajay/Documents/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> I can try running with System Integrity Protection off to see if that will
> make the -parallel tag work... any other thoughts?
>
>
> Thanks,
> Daniela
> ___
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Re: [Freesurfer] mri_vol2surf error in FS6

[zkaufman]

Hello Fred,

Do you have the /Applications/freesurfer/lib/gcc directory? Also, out of
curiosity, did freesurfer 5.3 exist on your system before installed 6.0?
That error shouldnt happen if FS6 is cleanly installed and definitely
shouldnt happen of SIPS is disabled.

I suppose as a last resort could you just completely remove FS from your
machine and just install it directly from the tar file (save the
license.txt file):

  
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz

  $> cp /Applications/freesurfer/license.txt ~
  $> sudo rm -rf /Applications/freesurfer
  $> sudo tar -C /Applications -xzvf
freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz
  $> sudo mv ~/license.txt /Applications/freesurfer/


> Dear FreeSurfer Experts,
>   I just installed FS6 and encountered the following error, which I can
> replicate by just entering “mri_vol2surf” on the command line:
>
> /Users/fred 3> mri_vol2surf
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> I am running Mac OS X El Capital 10.11.6, after searching the archives I
> also tried turning off SIP, which did not help.  Any  other advice?
>
> Thanks,
> Fred
>
>
> Fred Lado, MD PhD
> Director, Epilepsy - Central and Eastern Regions
> Northwell Health
> 917-608-1881 (mobile)
> 516-325-7000 (practice)
> 516-325-7001 (fax)
> fl...@northwell.edu
>
>
>
>
>
> Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527
> PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any
> attachments, is for the sole use of the intended recipient(s) and may
> contain confidential and privileged information. Any unauthorized review,
> use, disclosure or distribution is prohibited and may be unlawful. If you
> are not the intended recipient, please delete this e-mail immediately.
>
> ___
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Re: [Freesurfer] Building Freesurfer dev with GPU support/CUDA enabled

[zkaufman]

Hello Francis,

Yes, Richard is correct. When doing a local installation you will need the
freesurfer data files which do not come with a default clone of the repo.
Please see section 1.1 of the build page:

  $>
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

To get the data files required for installation, you need to type:

  $> $> git annex get --metadata fstags=makeinstall .

If you already did that and didnt get the file, its possibly missing the
tag (Ill have to double check). If that's the case, just get in manually:

  $> git annex get distribution/average/mult-comp-cor.tar.gz
  $> make install

-Zeke



  ## Get only the data files required for local installation (4.3 GB)
$> git annex get --metadata fstags=makeinstall .

> On 1 March 2017 at 03:28, Francis Tyson Thomas
>  wrote:
>
>> I have attached the log file as you had requested.
>
> This is the error:
> gzip: testdata.tar.gz: No such file or directory
> tar: This does not look like a tar archive
> tar: Exiting with failure status due to previous errors
> testdata: No such file or directory.
>
> I believe that git annex is supposed to supply the tarball... Zeke?
>
> Richard
> ___
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>
>
>

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Re: [Freesurfer] gzip: stdin: unexpected end of file

[zkaufman]

I just did a test download on my home network and I got the correct sha

  1723ef916c4e74ee8fff72438e9c6c91c79bd4cb 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz

Perhaps your network times out after a certain time period, or has a cap
on the file size?

> sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz returns
> da39a3ee5e6b4b0d3255bfef95601890afd80709
>
> A corrupted download three times! Do I just try downloading again?
>
> On Thu, Feb 23, 2017 at 9:02 AM 
> wrote:
>
>> Send Freesurfer mailing list submissions to
>> freesurfer@nmr.mgh.harvard.edu
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> or, via email, send a message with subject or body 'help' to
>> freesurfer-requ...@nmr.mgh.harvard.edu
>>
>> You can reach the person managing the list at
>> freesurfer-ow...@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. No FTP Access (Rockers, Elijah D.)
>>2. Re: No FTP Access (Rockers, Elijah D.)
>>3. Re: gzip: stdin: unexpected end of file (Z K)
>>4. Re: Re-running after Base Image Edits (Steros)
>>5. Re: FS 6.0 Freeview (peng)
>>6. Re: FS 6.0 Freeview (Kevin Aquino)
>>7. Virtualbox for FS v6.0 ? (Randolph Andrews)
>>8. recon-all error (6.0) (Trisanna Sprung-Much)
>>9. deformation fields (Worker, Amanda)
>>   10. How to output particular area from stats subdir (Jing Gu)
>>
>>
>>
>> -- Forwarded message --
>> From: "Rockers, Elijah D." 
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Cc:
>> Bcc:
>> Date: Wed, 22 Feb 2017 17:22:06 +
>> Subject: [Freesurfer] No FTP Access
>> Is there by any chance another way to download Freesurfer? My
>> institution does not allow FTP connections (HIPPA...) Same goes for the
>> tutorial data, but obviously Freesurfer is the priority here... thanks.
>>
>> - Eli
>>
>> Houston Methodist. Leading Medicine.
>>
>> U.S. News & World Report has recognized Houston Methodist as one of the
>> nation’s top 20 hospitals, placing it for the second time on the
>> magazine’s
>> prestigious Honor Roll. It is also designated as a Magnet hospital for
>> excellence in nursing. Visit us at houstonmethodist.org. Follow us at
>> twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.
>>
>> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston
>> Methodist Hospital and/or its relevant affiliates and may contain
>> restricted and privileged material for the sole use of the intended
>> recipient(s). Any review, use, distribution or disclosure by others is
>> strictly prohibited. If you are not the intended recipient (or
>> authorized
>> to receive for the recipient), please contact the sender and delete all
>> copies of the message. Thank you.
>>
>>
>>
>>
>>
>> -- Forwarded message --
>> From: "Rockers, Elijah D." 
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Cc:
>> Bcc:
>> Date: Wed, 22 Feb 2017 17:24:23 +
>> Subject: Re: [Freesurfer] No FTP Access
>> Nevermind. I discovered if I just change ftp to https in the download
>> link, it works fine.
>> - Eli
>>
>> On Wed, 2017-02-22 at 12:22 -0500, Elijah Rockers wrote:
>> > Is there by any chance another way to download Freesurfer? My
>> > institution does not allow FTP connections (HIPPA...) Same goes for
>> the
>> > tutorial data, but obviously Freesurfer is the priority here...
>> thanks.
>> >
>> > - Eli
>>
>>
>> Houston Methodist. Leading Medicine.
>>
>> U.S. News & World Report has recognized Houston Methodist as one of the
>> nation’s top 20 hospitals, placing it for the second time on the
>> magazine’s
>> prestigious Honor Roll. It is also designated as a Magnet hospital for
>> excellence in nursing. Visit us at houstonmethodist.org. Follow us at
>> twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.
>>
>> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston
>> Methodist Hospital and/or its relevant affiliates and may contain
>> restricted and privileged material for the sole use of the intended
>> recipient(s). Any review, use, distribution or disclosure by others is
>> strictly prohibited. If you are not the intended recipient (or
>> authorized
>> to receive for the recipient), please contact the sender and delete all
>> copies of the message. Thank you.
>>
>>
>>
>>
>>
>> -- Forwarded message --
>> From: Z K 
>> To: freesurfer@nmr.mgh.harvard.edu
>> Cc:
>> Bcc:
>> Date: Wed, 22 Feb 2017 12:54:38 -0500
>> Subject: Re: [Freesurfer] gzip: stdin: unexpected end of file
>> Its probably a corrupted download. What do you get when type 'sha1sum
>> 

Re: [Freesurfer] Talairach Registration Error : recon-all -s

[zkaufman]

This error is due to an incompatibility between the version of perl
shipped with ubuntu16 and the MINC tools shipped with freesurfer. This
issue has been fixed in freesurfer version 6.0, which I recommend you
download and install.

  https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

> It was actually mri_nu_correct.mni. this is our script that calls some
> MNIC programs. What version of MINC are you using?
>
>
> On 02/16/2017 01:01 PM, Dev vasu wrote:
>> Dear FreeSurfer Developers,
>>
>> I am incurring Talairach registration error when i was running recon-all
>> -s
>>
>> Error :
>>
>> recon-all -s KON2 exited with ERRORS at Do 16. Feb 16:23:10 CET 2017
>>
>>
>> Freesurfer Version :
>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
>> Platform: Ubuntu 16.04
>> recon-all log : see the attachment
>>
>>
>> Kindly let me know the problem with registration.
>>
>>
>> Thanks,
>> Vasudev
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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>
>
>

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Re: [Freesurfer] FreeSurfer stable v.6 Installation

[zkaufman]

If your question is whether you can install multiple versions of
freesurfer on your linux workstation, than the answer is yes. Just be sure
they are located in separate directories and be sure to set your
FREESURFER_HOME environment variable correctly.

-Zeke


> Dear FreeSurfer experts
>
> I would like to ask that whether or not I can install the package to the
> existing FS 5.3 that previously installed on our Linux system?
>
> Please forgive if it is an obvious question.
> Thanks
> *--v-- Peace --v--*
> *Duy Nguyễn *
> *Biomedical Engineering Department- IU HCMC*
> *Cell: (+84)90056*
> *Email: duy.nguyen...@gmail.com *
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Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

[zkaufman]

Hello Juhyoung,

If its complaining about "RB_all_2008-03-26.gca" then something must have
happened where you still have portions of the old freesurfer installed, or
your mixing versions because Freesurfer v6 has no mention of
RB_all_2008-03-26.gca. Please try completely removing the
/Applications/freesurfer directory and reinstalling v6.0.

If this doesnt work please email me the exact command and error output.



> Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer’, which I
> installed freesurfer v6.
> I attached recon-all.log file below.
> I can see 'build-stamp.txt:
> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ in log file.
>
> Is there anything to check more?
>
> Thank you,
> Juhyoung
>
>
>
>> On Feb 9, 2017, at 12:38 PM, Bruce Fischl 
>> wrote:
>>
>> sounds like you are using the old (5.2) recon-all. Are you sure it is 6
>> in your path?
>>
>> And can you email the list so others can answer?
>>
>> thanks
>> Bruce
>>
>>
>> On Thu, 9 Feb 2017, Juhyoung Ryu wrote:
>>
>>> Hi Bruce,
>>> I installed FREESURFER with version 6.0 for your recommendation and I
>>> got an
>>> error:
>>> mri_em_register: could not open GCA
>>> /Applications/freesurfer/average/RB_all_2008-03-26.gca.
>>> That file not exist in ‘average' folder, and there is one similar
>>> file: RB_all_2016-05-10.vc700.gca
>>>  Do you think I should drop that file manually from FREESURFER v5.2?
>>> Thank you in advance,Juhyoung
>>>
>>>  Begin forwarded message:
>>> From: Juhyoung Ryu 
>>> Subject: Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not
>>> finite at vno 0
>>> Date: February 8, 2017 at 11:01:23 AM GMT+9
>>> To: Z K 
>>> Cc: Bruce Fischl 
>>> Hi Zeke and Bruce,
>>> Thank you very much for your help.
>>> I’ll try it now and share the results.
>>> Thanks!
>>> Juhyoung.
>>>
>>>  On Feb 8, 2017, at 8:13 AM, Z K
>>>   wrote:
>>> Hello Juhyoung,
>>> I noticed from the recon-all.log files that you are using
>>> freesurfer v5.2. It was revealed that this version had issues
>>> regarding systematic white surface contraction and placement of
>>> the pial surface extending too far:
>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/029581.html
>>> I would recommend processing these subjects with version 6.0
>>>  https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>>> -Zeke
>>> On 02/06/2017 01:43 AM, Juhyoung Ryu wrote:
>>>
>>>  Hi FS developers,
>>>
>>>  I received errors in one of steps in recon-all.
>>>  I analyzed 111 individual subjects' T1 data using
>>>  same method, but there
>>>  are errors in _only 14 subjects._
>>>
>>>  Below is screenshot image in the end of
>>>  recon-all.log file. I attached
>>>  log files from two exemplar subjects below, also.
>>>
>>>  I’d appreciate if you might help me.
>>>  Juhyoung.
>>>
>>>  ___
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>>> The 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 Partners
>>> Compliance HelpLine at
>>> http://www.partners.org/complianceline . 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.
>
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Re: [Freesurfer] mri_mcsim OSX last version

[zkaufman]

The new version wont work in the FS5.3 framework. Its needs to be packaged
within the development version for it to work.

Whats the error? And does it only happen with one subject data, or all
subjects?

> Hi list,
> mri_mcsim on FS5.3 is giving a strange error in osx 10.11, in the wiki a
> newer Linux version is available and indicates to ask for other versions.
> Is it possible to have the last osx version?
> thanks!
> Gari
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Re: [Freesurfer] Freesurfer on Centos 7?

[zkaufman]

To get 5.3 working on machines with perl 5.22 or later I will refer you to
the following thread:

  https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50383.html

I cant say for sure how many mni scripts will need to point the the older
version of perl, its probably subjects dependant. But I would think it
would be 5 or less.

> Thanks for letting me know!
> What about v5.3?
> Do I merely need to replace nu_estimate_np_and_em and sharpen_volume, or
> is
> there anything else I would need to get it running?
> Caspar
>
>
> 2016-12-09 16:27 GMT-05:00 :
>
>>
>> The dev version of freesurfer (and the upcoming v6 release) is
>> compatible
>> with Centos7 and also fixes the perl/MNI issue.
>>
>>
>>
>> > Hi!
>> > I was wondering whether there is an update from the 2014 thread on
>> > Freesurfer's compatibility with Centos 7? The old thread is here:
>> > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
>> edu/msg38466.html
>> >
>> > I have also come across this website mentioning some changes in the
>> > installation related to Perl and MNI tools:
>> > http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7
>> >
>> > Any insights would be appreciated.
>> > Thanks, Caspar
>> > ___
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>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The 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 Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . 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.
>>
>>
>

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Re: [Freesurfer] Freesurfer on Centos 7?

[zkaufman]

The dev version of freesurfer (and the upcoming v6 release) is compatible
with Centos7 and also fixes the perl/MNI issue.



> Hi!
> I was wondering whether there is an update from the 2014 thread on
> Freesurfer's compatibility with Centos 7? The old thread is here:
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38466.html
>
> I have also come across this website mentioning some changes in the
> installation related to Perl and MNI tools:
> http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7
>
> Any insights would be appreciated.
> Thanks, Caspar
> ___
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Re: [Freesurfer] running freesurfer 5.3 on Ubuntu 16.04

[zkaufman]

Hello Peter,

I understand your dilemma, its unfortunate the updated version of perl
causes the MNI tools to fail. If you MUST use freesurfer 5.3 on an Ubuntu
16 machine there is only one way that I can think of to make it work:

You need to install perlbrew and use that to install perl version 5.20.3:

 $> sudo apt-get install perlbrew
 $> perlbrew install perl-5.20.3

You then must change the first line of any mni script that fails (their
should only be a few) to point to the perl v5.20 instead of the default.
So for example, the first line of $FREESURFER_HOME/mni/bin/nu_correct
should be changed from:

 #!/usr/bin/perl -w
to:
 #!~/perl5/perlbrew/perls/perl-5.20.3/bin/perl -w

You may need to do this with a couple of the MNI scripts. I know this is
not an ideal solution but it is the only way I know of to get
freesurfer5.3 working on Ubuntu 16.

-Zeke




> Hi,
>
> there is an old thread about an recon-all error on Ubuntu 16.04, that is
> caused by an incompatibility between the MNI tools and the perl version
> 5.22 distributed with Ubuntu 16.04.
>
> This has been fixed in the development version. Has someone a more
> detailed description how this was fixed so that I could try to back-port
> this fix to freesurfer 5.3?
>
> Downgrading perl in Ubuntu 16.04 is not possible, there are to many
> packages depending on it and there is no other version of perl in the
> repositories.
>
> We have already about 100 subjects analyzed with version 5.3 and I
> hesitate to re-analyze all of them with the development version.
>
> Since we had to update Ubuntu to 16.04 for other reasons, we use
> freesurfer 5.3 now inside a virtual machine with Ubuntu 14.04 installed,
> which is not very efficient.
>
> Peter
>
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>
>
>

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Re: [Freesurfer] 'Invalid' license file

[zkaufman]

We will be momentarily releasing a beta version of freesurfer version 6
that solves this issue. You can download and install that version which
will work on your opensuse 13.2 platform.

Otherwise you will need access to an older version of the libcrypt file
from opensuse 12.1 (which I dont have at the moment), see this response
from another user:

On 06/13/2013 03:07 AM, Claus Svarer wrote:
>
> So the solution for OpenSUSE 12.3 (64 bit) is to copy e.g.
> /lib64/libcrypt-2.14.1.so from an OpenSUSE 12.1 installation to
> /lib. and then make a symbolic link to that, like "ln
> -s libcrypt-2.14.1.so libcrypt.so.1" (also in /lib).
> Actually the LD_LIBRARY_PATH already included this directory (even two
> times) while I have the command "source
> $FREESURFER_HOME/SetUpFreeSurfer.sh" in the .profile (we are using bash
> shell).
>
> Thanks for the help
>
> Claus












> Hi,
>
> I have a similar problem. My opensuse version is 13.2. Could you help how
> to sovle this invilad license problem? Thanks.
>
> Best,
> Xiangzhen
>
>
> On Tue, Aug 16, 2016 at 3:05 PM,  wrote:
>
>> Hello Lee,
>>
>> Opensuse platforms versions greater than 12.1 are not compatible with
>> the
>> FreeSurfer licensing scheme, but their are workarounds. I will contact
>> you
>> offline so we can figure out the best solution for your setup.
>>
>> -Zeke
>>
>>
>>
>> > Hi,
>> > Our IT department have recently upgraded our cluster OS and now
>> Freesurfer
>> > complains that its license is invalid. I have tried rebuilding, and
>> > acquiring a new license, but these do not fix the problem. The license
>> > file I am using works in my Ubuntu 12.04 computer - it has been copied
>> > across as a file, not via a text editor - and used to work on an older
>> > version of the same OS.
>> >
>> > Do you know of any solution to this issue?
>> >
>> > I've tried everything I have seen on the mailing list, including
>> naming
>> it
>> > .license and license.txt, checking for whitespace, etc.
>> > Our OS is now SUSE Linux Enterprise Server 12 SP1 (x86_64).
>> >
>> > Many thanks,
>> > Lee
>> >
>> >
>> >
>> > ___
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>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The 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 Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . 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.
>>
>>
>
>
> --
> -
> Kong Xiangzhen
> State Key Laboratory of Cognitive Neuroscience and Learning,
> Beijing Normal University,
> Beijing, China, 100875.
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Re: [Freesurfer] CVS repository

[zkaufman]

This page should be more helpful for you.

  http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

-Zeke

> I am trying to checkout the development version of Freesurfer from the CVS
> repository.  I need to build against VTK 7.1 instead of 5.6 for freeview
> and am using these instructions:
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS
>
> Using this command:
>
>  cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot
> checkout -P dev
>
>
> Results in the following error:
>
>
> cvs server: cannot find module `dev' - ignored
>
> Can you tell me the correct module name?
>
>
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Re: [Freesurfer] differences between OS recon all output, longitudinal data

[zkaufman]

> Hi
>
> I am using recon-all in some longitudinal data on a ubuntu 16.04, and
> using
> the development version of freesurfer as I was told here, because the
> other
> current version doesnt work on ubuntu 16.04.
>
> The problem is that the first scans were probablly processed using
> virtualbox in a windows and an older version of freesurfer.
>
>
> i think I already know the answer, that I can't do this if I dont want to
> bias my results. Can I?

Yup. You know the answer ;) However, I did discover a way to make
freesurfer 5.3 work on Ubuntu 16 by doing the following steps to install
an older version of perl :

  1) install perlbrew:

$> sudo apt-get install perlbrew

  2) use perlbrew to install perl version 5.20.3:

$> perlbrew install perl-5.20.3

  3) You must change the '/bin/perl' file to a link which points to the
version of perl installed by perlbrew. (This technique is not the
standard practice but it is the only way to get the mni tools to use the
older version of perl):

$> cd /bin
$> sudo mv perl perl.orig (can always set back later)
$> ln -s ~/perl5/perlbrew/perls/perl-5.20.3/bin/perl


>
> But I'm using a better computer now and I use the one with windows for
> other analyses, so I wanted to know if I could install Virtual box on my
> ubuntu 16.04 computer, and install the same version of linux used to
> process the first measure. Should I also need to use the same version of
> freesurfer?


You could do that, but The Virtual Box version is not really good for
processing a large number of subjects because of the limited amount of
disk space on the virtual image. Its really meant more as a teaching tool
for users with Windows machines.

>
> f the computer's specs are dfferent, does it matter? And if I assign
> different cpu and ram on my virtual machine?

Different specs are fine. Its the OS, OS version,  and version of
freesurfer that should stay the same.


>
> Thank you!
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Re: [Freesurfer] Software License for Industry

[zkaufman]

The FreeSurfer Software License Agreement does not contain any language
explicitly or implicitly preventing commercial usage, however I will
highlight the following text from the License Agreement:

  "Any commercialization of the Software is at the sole risk
   of the party or parties engaged in such commercialization”

In short, commercial entities seeking to make use of FreeSurfer should
seek their own legal council on the interpretation of the license for
their specific circumstance.

-Zeke

> Dear FS experts
>
> I have one concern regarding the license and the Freesurfer usage on
> industry.
>
> We are setting up a start-up specialized with the analysis of brain MRI
> and
> we are interested on using FreeSurfer package as our main neuroimaging
> tool, due to the large amount of utilities it provides.
>
> After reading carefully the Software License provided here (
> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense) it is
> not clear for me if we could use yours software to provide a service to an
> external organisation/customer for which payment will be received.
>
> Could someone provide some insight on this issue?
>
> Bests,
> Joss.
>

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Re: [Freesurfer] malloc_error_break/ can't allocate region

[zkaufman]

Hello Paul,

Doug is essential correct. You can download 5.3 (or the development
version) and just extract it to a different location. Something like:

  $> mkdir /usr/local/freesurfer_5.3
  $> tar -C /usr/local/freesurfer_5.3 -xzvf
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

Then you are free to source either version - just make sure you to do in a
separate terminal window. Also, You can download freesurfer 5.3 or the
Development version (see "Development Version") from the following page:

  https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

Hope this helps.

-Zeke


> Zeke will know better than me, but I think the new version folder name
> will be different, so there should not be any conflict. You will just
> need to reference the new source file
>
> On 08/17/2016 12:23 PM, miracoo...@gmail.com wrote:
>> Sure. Also, do you know how I can upgrade to either without uninstalling
>> FS 5.1?
>>
>> Sent from my BlackBerry 10 smartphone.
>>Original Message
>> From: Douglas N Greve
>> Sent: Tuesday, August 16, 2016 4:01 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] malloc_error_break/ can't allocate region
>>
>> That sounds fishy. I would use the 5.3 or 6.0 version.
>>
>> On 08/16/2016 03:51 PM, miracle ozzoude wrote:
>>> FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.
>>>
>>> On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve
>>> > wrote:
>>>
>>> What version of FS (and mri_mcsim) are you using? Does it die if
>>> you run
>>> with just a few reps (eg, 100)?
>>>
>>> On 08/16/2016 01:21 PM, miracle ozzoude wrote:
 Hello FreeSurfer team,
 While running monte carlo correction with 1 reps (mri_mcsim) for
 the whole hemisphere, I received this error at 975 reps for the left
 hemisphere

 " 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216)
>>> failed
 (error code=12)
 *** error: can't allocate region
 *** set a breakpoint in malloc_error_break to debug
 Bus error"
 What does this mean and how can I resolve it? Below was my mri_mcsim
 command line " mri_mcsim --o
 wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base
 mc-z --surface fsaverage lh --nreps 1"

 Thank you
 Paul


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
>>> 
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu 
>>> Phone Number: 617-724-2358 
>>> Fax: 617-726-7422 
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> 
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> 
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> 
>>> Outgoing:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>> 
>>>
>>> ___
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>>> Freesurfer@nmr.mgh.harvard.edu 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>>
>>>
>>> The 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 Partners
>>> Compliance HelpLine at
>>> http://www.partners.org/complianceline
>>>  . 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.
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
>

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Re: [Freesurfer] 'Invalid' license file

[zkaufman]

Hello Lee,

Opensuse platforms versions greater than 12.1 are not compatible with the
FreeSurfer licensing scheme, but their are workarounds. I will contact you
offline so we can figure out the best solution for your setup.

-Zeke



> Hi,
> Our IT department have recently upgraded our cluster OS and now Freesurfer
> complains that its license is invalid. I have tried rebuilding, and
> acquiring a new license, but these do not fix the problem. The license
> file I am using works in my Ubuntu 12.04 computer - it has been copied
> across as a file, not via a text editor - and used to work on an older
> version of the same OS.
>
> Do you know of any solution to this issue?
>
> I've tried everything I have seen on the mailing list, including naming it
> .license and license.txt, checking for whitespace, etc.
> Our OS is now SUSE Linux Enterprise Server 12 SP1 (x86_64).
>
> Many thanks,
> Lee
>
>
>
> ___
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Re: [Freesurfer] mri_label2label holes

[zkaufman]

Hello Fred,

Yes, newer development binaries on Mac are not compatible with previous
releases of freesurfer. If you wish the use a newer binary you will need
to use the latest developmemnt version of freesurfer. This can be
downloaded from the following page (see "Development Version"):

  https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

Hoope this helps.

-Zeke


> Hi Fred, I think there are problems with trying to use v6 binaries
> without the v6 distribution. Zeke may have more of an idea.
>
> doug
>
>
> On 8/4/16 4:32 AM, Fred Dick wrote:
>> Dear Doug et al
>>
>> I was doing some cross-subject label morphing over a bunch of subjects
>> (a big continuous patch of vertices) and was having problems with
>> quite a number of 'missing' vertices in the morphed label.
>>
>> I saw Doug's previous response to this  on the message board that
>> there was a dev binary of label2label - I downloaded and tried but had
>> a bunch of dependency/lib errors (I'm running OSX).  Is there a new
>> version I should be looking at?
>>
>> Thanks as always!
>>
>> best
>> Fred
>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

[zkaufman]

Current versions of the Mac freesurfer binaries are not compatible with
the v5.3 release. Too much has changed since then. If you wanted to use
the newest version on the code you will need to download the latest dev
version of freesurfer from this page (see "Development Version"):

  https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download

Hope this helps.

-Zeke

> There was an obscure error having to do with the ascii header when
> unpacking skyra data on the mac, that might be it. Zeke, can you get
> Ismail a version of mri_convert appropriate for his OS?
>
> doug
>
>
>
> On 7/20/16 10:34 AM, Koubiyr, Ismail wrote:
>> Hi Doug,
>>
>> I tried it on the cluster and it worked, which is weird because it was
>> not working before … Any idea what might be the problem on my system ?
>> Thanks again.
>>
>> Ismail
>>
>>> On Jul 19, 2016, at 10:32 PM, Douglas Greve
>>> > wrote:
>>>
>>> I used the same version, but I used it on linux. Do you have a linux
>>> box with FS installed that you can try it on?
>>>
>>>
>>> On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
 I used the same command line as you did. And when I check with
 mri_probedicom I can see the ASCII header.

 Here is the version of FS I am using :
 freesurfer-i386-apple-darwin11.4.2-stable5-20130514

 Do you think it might be related ?

 Thanks again.

 Ismail

> On Jul 19, 2016, at 1:27 PM, Douglas N Greve
> > wrote:
>
> What is your exact command line?
>
> The version of the file that you gave me definitely has an ascii
> header,
> and I don't get that warning when I convert. What version of FS are
> you
> using on what platform? To check whether that file has an ascii
> header, run
>
> mri_probedicom --i
> MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
>
> There should be a line like below
>
> ### ASCCONV BEGIN
>
>
> On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
>> Hi Doug,
>>
>> That’s weird because I can’t convert it using only mri_convert, here
>> is the error I get :
>>
>> WARNING: file
>> /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
>> does not contain a Siemens ASCII header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>>
>> Any idea why ?
>>
>> Best,
>>
>> Ismail
>>
>>> On Jul 19, 2016, at 1:11 PM, Douglas N Greve
>>> >> >
>>> wrote:
>>>
>>> I was able to convert it fine with
>>> mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
>>> output.nii.gz
>>> If I included -it dicom, the conversion did not have an error,
>>> but the
>>> output had only one slice. Since these are mosaics, they need the
>>> Siemens ascii header which is ignored with -it dicom. So ...
>>> don't use
>>> -it dicom
>>>
>>>
>>> On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
 Hi Doug,

 It is still an issue. I uploaded the DICOMs to you. Hope it could
 be
 useful.
 Thanks.

 Ismail

> On Jul 18, 2016, at 6:14 PM, Douglas N Greve
>  >
> wrote:
>
> Is this still a problem? If so, can you upload the dicom files
> to our
> file drop?
>
> On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
>> The file has not been anonymized.
>>
>> Thanks,
>>
>> Ismail
>>
>>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve
>>> >> >
>>> wrote:
>>>
>>> can you answer the question that it asks?
>>>
>>> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
 Hi everyone,

 I’m having some issues converting my DICOMs (DWI) into NIFTI
 using
 mri_convert. I looked for other topics with people having
 the same
 kind of problem but couldn’t find an answer.

 Each time I run mri_convert on my DICOMs I get the following
 error :
 WARNING: file
 MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
 does not contain a Siemens ASCII header
 has this file been anonymized?
 ERROR: cannot unpack mosiacs without ASCII header

 Here are the following DICOMs 

Re: [Freesurfer] Building from source -- [wishlist] please version the -packages.tar.gz

[zkaufman]

Yes this is a good idea. All subsequent 3rd party bundles will be
versioned as (or similar to) the way you describe below. Which is good
because a new one will be released soon. Thanks for the input.

-Zeke

> ATM
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz
> has no versioned counterpart.  Could you please provide some versioning
> e.g. by actually having
>
> centos6-x86_64-packages-0.0.20151104.tar.gz  (based on its modification
> date, 0.0. to signal that it is not much of a real version), or
> following any other versioning scheme (e.g. base on version of
> freesurfer they were produced for)
>
> with
>
> centos6-x86_64-packages.tar.gz symlink pointing to it, so webserver (if
> FollowSymlinks) still resolving to that tarball
>
> Cheers,
> --
> Yaroslav O. Halchenko
> Center for Open Neuroscience http://centerforopenneuroscience.org
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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Re: [Freesurfer] Building from source #2 -- dynamic binding

[zkaufman]

Intolerable differences have not been found. They are always minor <%5 and
their source can come from several places. For example, different
compilers (or even different versions of the same compiler) can have
different sorting behavior when presented with objects that have
equivalent comparators. Others occur with data structures being
written/read to disk (Im still trying to fully understand those). As well
as a host of other potential differences as you mention below.

However, no cases have been found to fall outside expected and accepted
tolerance levels.

-Zeke




> On 20 February 2016 at 17:28, Bruce Fischl 
> wrote:
>
>> hmmm, the only thing that worries me about dynamic linking is that it
>> will add variability to the outputs. Zeke has spent endless amounts of
>> time
>> tracking down e.g. mac vs. pc differences in math libs and such.
>
> What sort of differences were found? Differences in transcendental
> functions are to be expected (so long as they are small) and lots of
> other things can cause slightly different results to be generated from
> floating point calculations (for instance, when summing an array, the
> result might vary with the number of OpenMP threads used). Were the
> segmentations produced intolerably different?
>
> Regards,
>
> Richard
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>
>

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Re: [Freesurfer] Building from source #2 -- dynamic binding

[zkaufman]

This topic gets brought up occasionally and their are valid arguments to
both sides. One reason we have hesitated to use dynamic libs is the partly
due to freesurfers long release cycle (all subjects that are part of a
study need to be performed all on the same version). This long release
cycle sometimes necessitates fixes to a particular binary in the stream,
which users are then free to use. Although this is a less than ideal
release strategy, it is the reality of the situation. And if we linked
against dynamic libs than any time a binary was updated, ALL those libs
would need to be updated, which in turn would affect all binaries which
link against them. I suppose only newly released binaries could be static,
but their may be unintended consequences that Im not thinking of at the
moment.

Im open to conversing about this, and appreciate any constructive feedback
on improving our release model. But I would prefer to take the
conversation offline as it gets overly technical rather quick.

-Zeke

>
> On Sat, 20 Feb 2016, Bruce Fischl wrote:
>
>> hmmm, the only thing that worries me about dynamic linking is that it
>> will add variability to the outputs. Zeke has spent endless amounts of
>> time
>> tracking down e.g. mac vs. pc differences in math libs and such. Won't
>> dynamic linking just make that a much more prevalent problem?
>
> nope -- I am not talking about dynamically linking external libraries
> ATM, but first about the internal ones, where the common code where
> instead of absorbing the same .a or .o blobs into multiple binaries,
> there would be a set of internal dynamic libraries which those
> binaries would be linked against, so there will no copies of
> binary code among different binaries.  I guess
> https://www.gnu.org/software/automake/manual/html_node/Libtool-Convenience-Libraries.html
> is a quick intro into those.
>
> As for linking against external libraries -- those could be bundled
> along with rpath pointing to their location or LD_LIBRARY_PATH
> override assuring they are picked up (instead of possibly available
> identically named system-wide ones).
>
> So overall it is possible to achieve absent variability while using
> dynamic linking and allowing for possibility of the flexibility ;)
>
> Cheers
> --
> Yaroslav O. Halchenko
> Center for Open Neuroscience http://centerforopenneuroscience.org
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik
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>
>
>

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Re: [Freesurfer] R: Re: Recon-all error

[zkaufman]

You need to provide input data for the subject. This would either go in
the 150622fracal/mri/orig folder or use the -i flag to point to the input
file.

-Zeke

> After this command
> recon-all -all -s 150622fracal -hippocampal-subfields-T1
>
> this error come out:
>
> Applications/freesurfer/subjects/150622fracal/scripts/recon-all.log
> Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0: Tue
> Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
> Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::
> Startup module) (@INC contains: /Applications/freesurfer/mni/lib/..
> /Library/Perl/Updates/5.10.0 /Library/Perl/5.18/darwin-thread-multi-
> 2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-
> multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2
> /System/Library/Perl/5.18/darwin-thread-multi-2level
> /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-
> thread-multi-2level /System/Library/Perl/Extras/5.18 .) at
> /Applications/freesurfer/mni/bin/nu_correct line 37.
> BEGIN failed--compilation aborted at
> /Applications/freesurfer/mni/bin/nu_correct line 37.
> #
> #@# MotionCor Sat Dec 26 12:57:51 CET 2015
> ERROR: no run data found in
> /Applications/freesurfer/subjects/150622fracal/mri. Make sure to
> have a volume called 001.mgz in
> /Applications/freesurfer/subjects/150622fracal/mri/orig.
> If you have a second run of data call it 002.mgz, etc.
> See also: http://surfer.nmr.mgh.harvard.
> edu/fswiki/FsTutorial/Conversion
> Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0: Tue
> Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
>
> recon-all -s 150622fracal exited with ERRORS at Sat Dec 26 12:57:51
> CET 2015
>
> For more details, see the log file
> /Applications/freesurfer/subjects/150622fracal/scripts/recon-all.log
> To report a problem, see http://surfer.nmr.mgh.harvard.
> edu/fswiki/BugReporting
>
>
>>Messaggio originale
>>Da: zkauf...@nmr.mgh.harvard.edu
>>Data: 26-dic-2015 1.03
>>A: "Freesurfer support list"
>>Cc: 
>>Ogg: Re: [Freesurfer] Recon-all error
>>
>>Hello Emad,
>>
>>  Thank you for reporting this. Its a bug specific to the latest
> version
>>of OS X (El Capitan). I have committed the fix and it will available
>>after the nightly build. You can download via this link:
>>
>>  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
>>
>>Sorry for the inconvenience and thanks for reporting.
>>
>>-Zeke
>>
>>
>>> Hi,
>>>
>>> I ran recon-all on the dicoms of a subject, obtained at Bay 4, and
> I
>>> received the following error:
>>>
>>> mris_calc -o lh.area.mid lh.area add lh.area.pial
>>> dyld: lazy symbol binding failed: Symbol not found:
> ___emutls_get_address
>>>   Referenced from:
>>> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>>>   Expected in: /usr/lib/libSystem.B.dylib
>>>
>>> dyld: Symbol not found: ___emutls_get_address
>>>   Referenced from:
>>> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>>>   Expected in: /usr/lib/libSystem.B.dylib
>>>
>>> Trace/BPT trap
>>> Wed Dec 23 21:59:54 EST 2015
>>> ERROR: vertexvol
>>> mris_calc -o lh.area.mid lh.area add lh.area.pial
>>> Darwin MGH000844.local 15.2.0 Darwin Kernel Version 15.2.0: Fri Nov
> 13
>>> 19:56:56 PST 2015; root:xnu-3248.20.55~2/RELEASE_X86_64 x86_64
>>>
>>> recon-all -s 3Lt_002 exited with ERRORS at Wed Dec 23 21:59:54 EST
> 2015
>>>
>>> For more details, see the log file
>>> /Users/Emad/Projects/3LT/subjDir/3Lt_002/scripts/recon-all.log
>>> To report a problem, see
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>
>>> I have attached the log file. I’d truly appreciate your help.
>>>
>>> Thank you, and with best wishes for a wonderful holiday season for
>>> everyone,
>>> Emad
>>>
>>>
>>> Emad Ahmadi, MD
>>> ---
>>> Research Fellow in Radiology
>>> Massachusetts General Hospital
>>> Harvard Medical School
>>>
>>> 25 New Chardon Street, Suite 400
>>> Boston, MA 02114
>>> Tel: 617 726 5237
>>> Email: e...@nmr.mgh.harvard.edu
>>>
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>___
>>Freesurfer mailing list
>>Freesurfer@nmr.mgh.harvard.edu
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>The 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 Partners Compliance
> HelpLine at
>>http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
>>but does not contain patient information, please contact the sender
> and properly

Re: [Freesurfer] R: Re: R: Re: Recon-all error

[zkaufman]

>From the recon-all wiki page under "specify input":

  https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Specifyinput

In this case you would use the -i flag to point to dicom file or nifti.
For example:

  recon-all -all -s 150622fracal -i 
-hippocampal-subfields-T1

-Zeke


> Hi Zeke,
> I'm sorry but I do not understand how run the correct command line.
> Where I should use --i?
> Thanks
>
>
> Stefano
>
>
>>Messaggio originale
>>Da: zkauf...@nmr.mgh.harvard.edu
>>Data: 26-dic-2015 21.50
>>A: , "Freesurfer support list" harvard.edu>
>>Cc: 
>>Ogg: Re: [Freesurfer] R: Re:  Recon-all error
>>
>>
>>You need to provide input data for the subject. This would either go
> in
>>the 150622fracal/mri/orig folder or use the -i flag to point to the
> input
>>file.
>>
>>-Zeke
>>
>>> After this command
>>> recon-all -all -s 150622fracal -hippocampal-subfields-T1
>>>
>>> this error come out:
>>>
>>> Applications/freesurfer/subjects/150622fracal/scripts/recon-all.log
>>> Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0:
> Tue
>>> Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64
> x86_64
>>> Can't locate MNI/Startup.pm in @INC (you may need to install the
> MNI::
>>> Startup module) (@INC contains: /Applications/freesurfer/mni/lib/..
>>> /Library/Perl/Updates/5.10.0 /Library/Perl/5.18/darwin-thread-
> multi-
>>> 2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-
>>> multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.
> 18.2
>>> /System/Library/Perl/5.18/darwin-thread-multi-2level
>>> /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-
>>> thread-multi-2level /System/Library/Perl/Extras/5.18 .) at
>>> /Applications/freesurfer/mni/bin/nu_correct line 37.
>>> BEGIN failed--compilation aborted at
>>> /Applications/freesurfer/mni/bin/nu_correct line 37.
>>> #
>>> #@# MotionCor Sat Dec 26 12:57:51 CET 2015
>>> ERROR: no run data found in
>>> /Applications/freesurfer/subjects/150622fracal/mri. Make sure to
>>> have a volume called 001.mgz in
>>> /Applications/freesurfer/subjects/150622fracal/mri/orig.
>>> If you have a second run of data call it 002.mgz, etc.
>>> See also: http://surfer.nmr.mgh.harvard.
>>> edu/fswiki/FsTutorial/Conversion
>>> Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0:
> Tue
>>> Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64
> x86_64
>>>
>>> recon-all -s 150622fracal exited with ERRORS at Sat Dec 26 12:57:51
>>> CET 2015
>>>
>>> For more details, see the log file
>>> /Applications/freesurfer/subjects/150622fracal/scripts/recon-all.
> log
>>> To report a problem, see http://surfer.nmr.mgh.harvard.
>>> edu/fswiki/BugReporting
>>>
>>>
Messaggio originale
Da: zkauf...@nmr.mgh.harvard.edu
Data: 26-dic-2015 1.03
A: "Freesurfer support list"
Cc: 
Ogg: Re: [Freesurfer] Recon-all error

Hello Emad,

  Thank you for reporting this. Its a bug specific to the latest
>>> version
of OS X (El Capitan). I have committed the fix and it will
> available
after the nightly build. You can download via this link:

  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/

Sorry for the inconvenience and thanks for reporting.

-Zeke


> Hi,
>
> I ran recon-all on the dicoms of a subject, obtained at Bay 4,
> and
>>> I
> received the following error:
>
> mris_calc -o lh.area.mid lh.area add lh.area.pial
> dyld: lazy symbol binding failed: Symbol not found:
>>> ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> Trace/BPT trap
> Wed Dec 23 21:59:54 EST 2015
> ERROR: vertexvol
> mris_calc -o lh.area.mid lh.area add lh.area.pial
> Darwin MGH000844.local 15.2.0 Darwin Kernel Version 15.2.0: Fri
> Nov
>>> 13
> 19:56:56 PST 2015; root:xnu-3248.20.55~2/RELEASE_X86_64 x86_64
>
> recon-all -s 3Lt_002 exited with ERRORS at Wed Dec 23 21:59:54
> EST
>>> 2015
>
> For more details, see the log file
> /Users/Emad/Projects/3LT/subjDir/3Lt_002/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> I have attached the log file. I’d truly appreciate
> your
> help.
>
> Thank you, and with best wishes for a wonderful holiday season
> for
> everyone,
> Emad
>
>
> Emad Ahmadi, MD
> ---
> Research Fellow in Radiology
> 

Re: [Freesurfer] Recon-all error

[zkaufman]

Hello Emad,

  Thank you for reporting this. Its a bug specific to the latest version
of OS X (El Capitan). I have committed the fix and it will available
after the nightly build. You can download via this link:

  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/

Sorry for the inconvenience and thanks for reporting.

-Zeke


> Hi,
>
> I ran recon-all on the dicoms of a subject, obtained at Bay 4, and I
> received the following error:
>
> mris_calc -o lh.area.mid lh.area add lh.area.pial
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> Trace/BPT trap
> Wed Dec 23 21:59:54 EST 2015
> ERROR: vertexvol
> mris_calc -o lh.area.mid lh.area add lh.area.pial
> Darwin MGH000844.local 15.2.0 Darwin Kernel Version 15.2.0: Fri Nov 13
> 19:56:56 PST 2015; root:xnu-3248.20.55~2/RELEASE_X86_64 x86_64
>
> recon-all -s 3Lt_002 exited with ERRORS at Wed Dec 23 21:59:54 EST 2015
>
> For more details, see the log file
> /Users/Emad/Projects/3LT/subjDir/3Lt_002/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> I have attached the log file. I’d truly appreciate your help.
>
> Thank you, and with best wishes for a wonderful holiday season for
> everyone,
> Emad
>
>
> Emad Ahmadi, MD
> ---
> Research Fellow in Radiology
> Massachusetts General Hospital
> Harvard Medical School
>
> 25 New Chardon Street, Suite 400
> Boston, MA 02114
> Tel: 617 726 5237
> Email: e...@nmr.mgh.harvard.edu
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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The information in this e-mail is intended only for the person to whom it is
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dispose of the e-mail.

Re: [Freesurfer] freesurfer 6 error: dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib

[zkaufman]

Did you source the Freesurfer setup script?

  $> export FREESURFER_HOME=/Applications/freesurfer6
  $> source $FREESURFER_HOME/SetUpFreeSurfer.sh




> Hello All,
>
> I installed freesurfer 6 on a mac running OS-X Yosemite 10.10.4. I am
> getting the following error when I run recon-all from freesurfer 6.
>
> Can you please suggest how to fix it ?
>
> Thank you,
>
> Ri
>
> ri@Magi [0] ~/ri/SampleDatasets$ export
> FREESURFER_HOME= ;export
> SUBJECTS_DIR=/Applications/freesurfer6/subjects;export
> PATH=/Applications/freesurfer6/bin:$PATH;/Applications/freesurfer6/bin/recon-all
> -s Dataset1-only-T1 -i Dataset1/MPRAGE.nii.gz -all
> Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015
> Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015
> INFO: SUBJECTS_DIR is /Applications/freesurfer6/subjects
> Actual FREESURFER_HOME /Applications/freesurfer6
> Darwin Magi.uphs.upenn.edu 14.4.0 Darwin Kernel Version 14.4.0: Thu May 28
> 11:35:04 PDT 2015; root:xnu-2782.30.5~1/RELEASE_X86_64 x86_64
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_convert
>   Reason: image not found
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_convert
>   Reason: image not found
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_make_uchar
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_normalize
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_watershed
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_gcut
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_segment
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_label2label
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_em_register
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_ca_normalize
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_ca_register
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_ca_label
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_pretess
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_fill
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_tessellate
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_concatenate_lta
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_normalize_tp2
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_smooth
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_inflate
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_curvature
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_sphere
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_fix_topology
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_topo_fixer
>   

Re: [Freesurfer] ERROR: Invalid FreeSurfer license key

[zkaufman]

Hello Neda,

Hello Neda,

Can you please send me an email with a copy of your .license file as an
attachment? *Please send it to my direct email address* and not to the
Freesurfer support list. I will take a look and send you a valid license
file if necessary.

-Zeke



> Hi Bruce,
>
> I'm sure about it, but I get the error.
>
> *Best Regards,*
> *Neda*
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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The 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 Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

[zkaufman]

There were some recent changes in the build that eliminated the necessity
for that library. Casper, can you try using this most recent version and
let me know if it works?

  
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_coreg

Thanks,

-Zeke


> Zeke, is this a new library that we need for v6?
> doug
>
> On 11/20/2015 09:42 AM, Caspar M. Schwiedrzik wrote:
>> Hi Doug,
>> when I try to execute mri_coreg, I get the following error message:
>>
>> error while loading shared libraries: libnetcdf.so.6: cannot open
>> shared object file: no such file or directory
>>
>> Caspar
>>
>>
>> 2015-11-19 18:49 GMT-05:00 Douglas Greve > >:
>>
>>
>> Can you try mri_coreg instead of fsl?
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>>
>>
>>
>>
>> On 11/19/15 5:25 PM, Caspar M. Schwiedrzik wrote:
>>> Hi!
>>> I am trying to align a mean EPI volume and a Bruker magnitude map
>>> from a fieldmap measurement using tkregister2, fsl_rigid_register
>>> and mri_vol2vol. Unfortunately, it seems that somewhere, most
>>> likely during fsl_rigid_register, the image orientation get
>>> scrambled, and the output has the wrong orientation.
>>>
>>> Here is what I get from*tkregister2:*
>>>
>>> target  volume epi.nii
>>> movable volume fieldmap0001.nii
>>> reg file mag_2_mocovol.register.dat
>>> LoadVol0
>>> ZeroCRAS   0
>>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
>>> Diagnostic Level -1
>>> INFO: loading target epi.nii
>>> Setting targ orientation to RIA
>>> INFO: target does not conform to COR format, so I'm going to
>>> reslice to COR. This will not affect the final registration.
>>> Ttarg: 
>>> -1.000   0.000   0.000 128.000;
>>>  0.000   0.000   1.000 -128.000;
>>>  0.000  -1.000   0.000 128.000;
>>>  0.000   0.000   0.000   1.000;
>>> INFO: loading movable fieldmap0001.nii
>>> Setting mov orientation to RIA
>>> Tmov: 
>>> -0.547   0.000   0.000   17.500;
>>>  0.000   0.000   0.547  -17.500;
>>>  0.000  -0.547   0.000   17.500;
>>>  0.000   0.000   0.000   1.000;
>>> mkheaderreg = 1, float2int = 0
>>> Computing reg from header (and possibly input matrix)
>>>  Input registration matrix (computed) 
>>> -1.000   0.000   0.000  -0.587;
>>>  0.000   1.000   0.000  -2.150;
>>>  0.000   0.000   1.000  -2.188;
>>>  0.000   0.000   0.000   1.000;
>>> ---
>>>  Input registration matrix 
>>> -1.000   0.000   0.000  -0.587;
>>>  0.000   1.000   0.000  -2.150;
>>>  0.000   0.000   1.000  -2.188;
>>>  0.000   0.000   0.000   1.000;
>>> Determinant -1
>>> subject = rat
>>> RegMat ---
>>>  1.000   0.000   0.000  -0.587;
>>>  0.000   1.000   0.000  -2.150;
>>>  0.000   0.000   1.000  -2.188;
>>>  0.000   0.000   0.000   1.000;
>>> FSLOUTPUTTYPE NIFTI_GZ
>>> tkreg2FSL: mov det = 0.163555, ref det = 0.154688
>>> INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det,
>>>   applying LR flip to registration matrix.
>>> INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det,
>>>   applying LR flip to registration matrix.
>>>
>>> here is what I get from fsl_rigid_register:
>>> $Id: fsl_rigid_register,v 1.31 2011/03/02 20:16:39 nicks Exp $
>>> Thu Nov 19 17:13:48 EST 2015
>>> fieldmap0001_reg.nii
>>> Reference is nifti, not converting
>>> Input is nifti, not converting
>>> Output is nifti, not converting
>>> --
>>> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap
>>> calling eval flirt.fsl -in ./fieldmap0001.hdr -out
>>> ./fieldmap0001_reg.hdr -bins 256 -cost corratio -searchrx -10 10
>>> -searchry -10 10 -searchrz -10 10 -interp trilinear -dof 6 -ref
>>> ./epi.hdr -init initxfm.fslmat -omat ./fieldmap0001_reg.fslmat
>>> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap
>>> mri_copy_params --pulse fieldmap0001_reg.nii fieldmap0001.nii
>>> fieldmap0001_reg.nii
>>> only copying pulse parameters
>>> WARNING: volume sizes are different
>>> in_vol : 80, 80, 22
>>>   temp_vol : 64, 64, 64
>>> WARNING: voxel sizes are different
>>> in_vol : 0.375, 0.375, 1.1
>>>   temp_vol : 0.546875, 0.546875, 0.546875
>>> --
>>> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap
>>> tkregister2_cmdl --targ epi.nii --mov fieldmap0001.nii --reg
>>> ./fsl_rigid_register.28592/reg.dat --fslreg
>>> fieldmap0001_reg.nii.fslmat --noedit
>>> tkregister_tcl
>>> 
>>> 

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

[zkaufman]

Oh, Sorry about that, I was unaware you were using freesurfer v5.1 on an
older RedHat system.

Freesurfer v5.1 was released quite awhile ago and its entirely possible
that the newest development version of the freesurfer binaries are not
compatible with it. But here is a link to our centos4 build which in
theory has the best shot of working on your system:

  
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos4_x86_64/mri_coreg

Please give it a shot, and sorry for the initial confusion.

-Zeke





> Red Hat Enterprise Linux Server release 5.9 (Tikanga)
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>
> Caspar
>
>
> 2015-11-23 14:37 GMT-05:00 :
>
>> What system are you running on? Also, what are the contents of your
>> build-stamp.txt file (in your FREESURFER_HOME directory)?
>>
>> -Zeke
>>
>>
>> > Hi Zeke,
>> > I tried the is new version. Now I am getting:
>> >
>> > mri_coreg: /lib64/libuuid.so.1: no version information available
>> (required
>> > by mri_coreg)
>> > mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
>> found
>> > (required by mri_coreg)
>> > mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
>> found
>> > (required by mri_coreg)
>> > mri_coreg: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
>> by
>> > mri_coreg)
>> >
>> > Caspar
>> >
>> >
>> > 2015-11-23 14:20 GMT-05:00 :
>> >
>> >> There were some recent changes in the build that eliminated the
>> >> necessity
>> >> for that library. Casper, can you try using this most recent version
>> and
>> >> let me know if it works?
>> >>
>> >>
>> >>
>> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_coreg
>> >>
>> >> Thanks,
>> >>
>> >> -Zeke
>> >>
>> >>
>> >> > Zeke, is this a new library that we need for v6?
>> >> > doug
>> >> >
>> >> > On 11/20/2015 09:42 AM, Caspar M. Schwiedrzik wrote:
>> >> >> Hi Doug,
>> >> >> when I try to execute mri_coreg, I get the following error
>> message:
>> >> >>
>> >> >> error while loading shared libraries: libnetcdf.so.6: cannot open
>> >> >> shared object file: no such file or directory
>> >> >>
>> >> >> Caspar
>> >> >>
>> >> >>
>> >> >> 2015-11-19 18:49 GMT-05:00 Douglas Greve
>> > >> >> >:
>> >> >>
>> >> >>
>> >> >> Can you try mri_coreg instead of fsl?
>> >> >>
>> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> On 11/19/15 5:25 PM, Caspar M. Schwiedrzik wrote:
>> >> >>> Hi!
>> >> >>> I am trying to align a mean EPI volume and a Bruker magnitude
>> >> map
>> >> >>> from a fieldmap measurement using tkregister2,
>> >> fsl_rigid_register
>> >> >>> and mri_vol2vol. Unfortunately, it seems that somewhere, most
>> >> >>> likely during fsl_rigid_register, the image orientation get
>> >> >>> scrambled, and the output has the wrong orientation.
>> >> >>>
>> >> >>> Here is what I get from*tkregister2:*
>> >> >>>
>> >> >>> target  volume epi.nii
>> >> >>> movable volume fieldmap0001.nii
>> >> >>> reg file mag_2_mocovol.register.dat
>> >> >>> LoadVol0
>> >> >>> ZeroCRAS   0
>> >> >>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp
>> $
>> >> >>> Diagnostic Level -1
>> >> >>> INFO: loading target epi.nii
>> >> >>> Setting targ orientation to RIA
>> >> >>> INFO: target does not conform to COR format, so I'm going to
>> >> >>> reslice to COR. This will not affect the final registration.
>> >> >>> Ttarg: 
>> >> >>> -1.000   0.000   0.000 128.000;
>> >> >>>  0.000   0.000   1.000 -128.000;
>> >> >>>  0.000  -1.000   0.000 128.000;
>> >> >>>  0.000   0.000   0.000   1.000;
>> >> >>> INFO: loading movable fieldmap0001.nii
>> >> >>> Setting mov orientation to RIA
>> >> >>> Tmov: 
>> >> >>> -0.547   0.000   0.000   17.500;
>> >> >>>  0.000   0.000   0.547  -17.500;
>> >> >>>  0.000  -0.547   0.000   17.500;
>> >> >>>  0.000   0.000   0.000   1.000;
>> >> >>> mkheaderreg = 1, float2int = 0
>> >> >>> Computing reg from header (and possibly input matrix)
>> >> >>>  Input registration matrix (computed) 
>> >> >>> -1.000   0.000   0.000  -0.587;
>> >> >>>  0.000   1.000   0.000  -2.150;
>> >> >>>  0.000   0.000   1.000  -2.188;
>> >> >>>  0.000   0.000   0.000   1.000;
>> >> >>> ---
>> >> >>>  Input registration matrix 
>> >> >>> -1.000   0.000   0.000  -0.587;
>> >> >>>  0.000   1.000   0.000  -2.150;
>> >> >>>  0.000   0.000   1.000  -2.188;
>> >> >>>  0.000   0.000   0.000   1.000;
>> >> >>> Determinant -1
>> >> >>> subject = rat
>> >> >>> RegMat ---
>> >> >>>  1.000   0.000   0.000  -0.587;
>> 

Re: [Freesurfer] trac-all and mri_convert and FS license

[zkaufman]

This is an unfortunate consequence of mixing and matching various
subcomponents of freesurfer. I will private message you a potential work
around.

-Zeke


> Dear FS experts
>
> we are running TRACULA on a Mac (OS X 10.7.5) and faced an error related
> to mri_convert.
>
> we then donloaded (as suggested in the FS archives) the modified file
> mri_convert.mac from here
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> and the initial error disappeared.
>
> However, when running trac-all FS claims that the license is not valid
> anymore, although there is no error when running
> recon-all.
>
> [Tschgiallos-iMac-2:~] tschgiallo% trac-all -prep -c
> /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/tracula_config_dudo.txt
> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
> INFO: Diffusion root is
> /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results
> Actual FREESURFER_HOME /Applications/freesurfer
> trac-preproc -c
> /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results/0028197/scripts/dmrirc.local
> -log
> /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results/0028197/scripts/trac-all.log
> -cmd
> /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results/0028197/scripts/trac-all.cmd
> #-
> /Applications/freesurfer/bin/trac-preproc
> #-
> #@# Image corrections Mo 16 Nov 2015 09:57:39 CET
> mri_convert
> /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/prepare/0028197/0028197_dti.nii.gz
> /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results/0028197/dmri/dwi_orig.nii.gz
> mri_convert
> /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/prepare/0028197/0028197_dti.nii.gz
> /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results/0028197/dmri/dwi_orig.nii.gz
> --
> ERROR: Invalid FreeSurfer license key found in license file
> /Applications/freesurfer/.license
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
> --
> $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $
> reading from
> /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/prepare/0028197/0028197_dti.nii.gz...
> Darwin Tschgiallos-iMac-2.local 11.4.2 Darwin Kernel Version 11.4.2: Thu
> Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
>
> trac-preproc exited with ERRORS at Mo 16 Nov 2015 09:57:40 CET
>
> [Tschgiallos-iMac-2:~] tschgiallo%
>
>
> Any idea where the problem is?
>
> Thanks in advance
> Regards
> Jürgen
>
> -
> University of Zurich
> Dr. Jürgen Hänggi, Ph.D.
> Department of Psychology
> Division Neuropsychology
> Binzmuehlestrasse 14, PO Box 25
> 8050 Zurich, Switzerland
>
> 0041 44 635 73 97 (phone office)
> 0041 76 445 86 84 (phone mobile)
> 0041 44 635 74 09 (fax office)
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>
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> http://www.juergenhaenggi.ch (private website)
>
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Re: [Freesurfer] Issue opening .dmg file for installing freesurfer patch/code addition for brainstem. Error is "image not recognized"

[zkaufman]

My guess is that you are using Safari on a Mac OSX Machine? If so, I have
observed that Safari  has strange behavior with ftp links. Can you try
using another browser like Firefox or Chrome? Or, you can download by
typing the following command in a terminal window:

  $> curl -O
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-OSX-dev.dmg

Hope this helps.

-Zeke


> Hello,
>
> I'm trying to segment the brainstem into subparts. I found online for
> freesurfer 5.3 you can use the following link to install the need codes:
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
>
>
> which was from the following freesurfer question/solution:
>
>
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42064.html
>
> However, when I open the ftp as a guest and try to open the .dmg file I
> get
> the error "image not recognized". Looking into why this happens it sounds
> like the download went bad. I've tried re-downloading the file a few times
> and am now wondering if the uploaded file was bad? Is there another
> solution so I can segment the brainstem?
>
> Thank you for your help,
>
> Jon
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Re: [Freesurfer] Compiling dev version in ubuntu 15.10

[zkaufman]

Is is a warning or an error?

Passing the --disable-Werror flag to the configure script will prevent the
build from erroring out if it comes across a warning from the compiler. I
havent testing on Ubuntu 15 but I will give it a shot early early next
week.

-Zeke

> I'm preparing to migrate over to the new Ubuntu when it comes out.
>
> I'm having the following issues compiling it:
>
> The included VXL library doesnt compile, using the system version seems to
> fix this:
>
> /usr/pubsw/packages/vxl/current/include/vxl/core/vnl/algo/vnl_symmetric_eigensystem.h:82:1:
> warning: keyword 'export' not implemented, and will be ignored
> export template 
>
> The inline functions MRIgetVoxVal ... should be defined in the .h file,
> they are not, I have to comment out the inline versions
>
> ../include/mri.h:313:15: warning: inline function 'MRIgetVoxVal' declared
> but never defined
> inline float  MRIgetVoxVal(const MRI *mri, int c, int r, int s, int f);
>
> The included ITK library doesnt have the cxx11 ABI
> ../utils/libutils.a(mriio_nrrd_itk.o): In function
> `itk::MemoryAllocationError::MemoryAllocationError(std::__cxx11::basic_string std::char_traits, std::allocator > const&, unsigned int,
> std::__cxx11::basic_string std::allocator > const&, std::__cxx11::basic_string std::char_traits, std::allocator > const&)':
> /usr/pubsw/packages/itk/current/include/InsightToolkit/Common/itkExceptionObject.h:174:
> undefined reference to
> `itk::ExceptionObject::ExceptionObject(std::__cxx11::basic_string std::char_traits, std::allocator > const&, unsigned int,
> std::__cxx11::basic_string std::allocator > const&, std::__cxx11::basic_string std::char_traits, std::allocator > const&)'
> ../utils/libutils.a(mriio_nrrd_itk.o):(.rodata._ZTVN3itk24ImageFileReaderExceptionE[_ZTVN3itk24ImageFileReaderExceptionE]+0x40):
> undefined reference to
> `itk::ExceptionObject::SetLocation(std::__cxx11::basic_string std::char_traits, std::allocator > const&)'
> ../utils/libutils.a(mriio_nrrd_itk.o):(.rodata._ZTVN3itk24ImageFileReaderExceptionE[_ZTVN3itk24ImageFileReaderExceptionE]+0x48):
> undefined reference to
> `itk::ExceptionObject::SetDescription(std::__cxx11::basic_string std::char_traits, std::allocator > const&)'
> ../utils/libutils.a(mriio_nrrd_itk.o):(.rodata._ZTVN3itk21MemoryAllocationErrorE[_ZTVN3itk21MemoryAllocationErrorE]+0x40):
> undefined reference to
> `itk::ExceptionObject::SetLocation(std::__cxx11::basic_string std::char_traits, std::allocator > const&)'
> ../utils/libutils.a(mriio_nrrd_itk.o):(.rodata._ZTVN3itk21MemoryAllocationErrorE[_ZTVN3itk21MemoryAllocationErrorE]+0x48):
> undefined reference to
> `itk::ExceptionObject::SetDescription(std::__cxx11::basic_string std::char_traits, std::allocator > const&)'
> ../utils/libutils.a(mriio_nrrd_itk.o): In function
> `itk::ImageFileReader,
> itk::DefaultConvertPixelTraits
> >::GenerateOutputInformation()':
> /usr/pubsw/packages/itk/current/include/InsightToolkit/IO/itkImageFileReader.txx:136:
> undefined reference to
> `itk::ObjectFactoryBase::CreateAllInstance[abi:cxx11](char const*)'
> ../utils/libutils.a(mriio_nrrd_itk.o): In function
> `itk::ImageFileReader,
> itk::DefaultConvertPixelTraits
> >::DoConvertBuffer(void*, unsigned long)':
> /usr/pubsw/packages/itk/current/include/InsightToolkit/IO/itkImageFileReader.txx:545:
> undefined reference to
> `itk::ImageIOBase::GetComponentTypeAsString[abi:cxx11](itk::ImageIOBase::IOComponentType)
> const'
> ../utils/libutils.a(numerics.o):(.rodata._ZTV8fs_lbfgs[_ZTV8fs_lbfgs]+0x28):
> undefined reference to `vnl_nonlinear_minimizer::is_a[abi:cxx11]() const'
> ../utils/libutils.a(numerics.o):(.rodata._ZTV8fs_lbfgs[_ZTV8fs_lbfgs]+0x30):
> undefined reference to
> `vnl_nonlinear_minimizer::is_class(std::__cxx11::basic_string std::char_traits, std::allocator > const&) const'
> ../utils/libutils.a(numerics.o):(.rodata._ZTV9fs_powell[_ZTV9fs_powell]+0x28):
> undefined reference to `vnl_nonlinear_minimizer::is_a[abi:cxx11]() const'
> ../utils/libutils.a(numerics.o):(.rodata._ZTV9fs_powell[_ZTV9fs_powell]+0x30):
> undefined reference to
> `vnl_nonlinear_minimizer::is_class(std::__cxx11::basic_string std::char_traits, std::allocator > const&) const'
>
>
>
> Dr Chris Adamson
> Research Officer, Developmental Imaging, Murdoch Childrens Research
> Institute
> Murdoch Childrens Research Institute
> Royal Children's Hospital
> Flemington Road, Parkville, Victoria  3052, Australia
> www.mcri.edu.au
> E   chris.adam...@mcri.edu.au
> T   03 9936 6780
>
>
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> This email has been scanned by the Symantec Email Security.cloud service.
> For more information please visit http://www.symanteccloud.com
> 

Re: [Freesurfer] Freeview.bin - error while loading shared libraries: libvtkverdict.so.5.6 cannot open sharted ...

[zkaufman]

Hello,

This is a known when running freesurfer on Ubuntu systems. The solution is
addressed in the FAQ section on the frresurfer download page:

  https://surfer.nmr.mgh.harvard.edu/fswiki/Download

pecifically, the solution is to go into you system's lib directory and
create a symlink as follows:

  $> cd /usr/lib/x86_64 (or something similar depending upon exact version)
  $> sudo ln -s libjpeg.so.8 libjpeg.so.62
  $> sudo ln -s libtiff.so.4 libtiff.so.3

This should solve it. Best,

-Zeke



> Dear colleagues,
> I'm installing Freesurfer-Linux-CentOS4-stable-pub-v5.3.0 on Ubuntu 14.04
> LTS (updated) and I managed to make tkmedit run correctly, but when I try
> QDEC and Freeview I'm getting this message:
> "qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot
> open
> shared object file: No such fie or directory
> and
> "freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot
> open shared object file: No such file or directory"
>
> Any ideas or suggestions of what I might have done wrong?
> Thank you very much
> Best,
> Felipe Picon
>
> 2015-04-06 19:04 GMT-03:00 Johannes Kaufhold
> 
> :
>
>> Hi Zeke,
>>
>> I managed to solve this issue.
>>
>> I have changed the ownership of all folders and files in
>> /usr/local/freesurfer to my Ubuntu user name and now Freeview is working
>> with the sample data.
>>
>> ..Just seeing your email coming in.
>>
>> Best,
>> jk
>>
>> On 06/04/15 22:34, Johannes Kaufhold wrote:
>> > Hi Zeke,
>> >
>> > Yes, I'm attempting to open freeview in the same terminal window in
>> > which I have sourced SetUpFreeSurfer.csh.
>> >
>> > Here's the output from ls -l
>> > $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict*
>> >
>> > lrwxrwxrwx 1 root root 22 May 13  2013
>> > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so ->
>> > libvtkverdict.so.5.6.0
>> > lrwxrwxrwx 1 root root 22 May 13  2013
>> > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 ->
>> > libvtkverdict.so.5.6.0
>> > -rwsrwsr-t 1 root root 189017 Aug 17  2010
>> > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0
>> >
>> > Best,
>> > Johannes
>> >
>> > On 06/04/15 21:48, Z K wrote:
>> >> Hello Johannes,
>> >>
>> >> You are attempting to open freeview *in the same window* that you
>> >> sourced SetUpFreeSurfer.csh(sh), correct? Also, can you tell me what
>> the
>> >> output of the terminal is when you type the following command:
>> >>
>> >> ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict*
>> >>
>> >> -Zeke
>> >>
>> >> On 04/06/2015 04:32 PM, Johannes Kaufhold wrote:
>> >>> Hi all,
>> >>>
>> >>> I'm super new to Freesurfer. I just set it up on my computer earlier
>> >>> today, following the official wiki on harvard.edu/fswiki...
>> >>>
>> >>> My system:
>> >>> - Ubuntu 14.04 LTS (up to date)
>> >>> - Tcsh installed
>> >>> - Freesurfer version:
>> >>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
>> >>> <
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
>> >
>> >>> - Mathlab not installed
>> >>>
>> >>> Sourcing the SetUpFreeSurfer.csh(sh) script worked fine and
>> license.txt
>> >>> is in $FREESURFER_HOME.
>> >>>
>> >>> When trying to pull and view the sample data by entering the below
>> in
>> >>> the terminal (tcsh)
>> >>>
>> >>> freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v
>> >>> $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
>> >>> $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
>> >>> $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
>> >>> $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
>> >>> $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
>> >>>
>> >>> I'm getting the following error message*
>> >>> **
>> >>> **freeview.bin: error while loading shared libraries:
>> >>> libvtkverdict.so.5.6: cannot open shared object file: No such file
>> or
>> >>> directory*
>> >>>
>> >>> I was searching for the missing file in Aptitude and on the
>> internet,
>> >>> but couldn't manage to find it.
>> >>>
>> >>> Any suggestions how to proceed from here?
>> >>>
>> >>> Thanks and best wishes!
>> >>> Johannes
>> >>>
>> >>>
>> >>> ___
>> >>> Freesurfer mailing list
>> >>> Freesurfer@nmr.mgh.harvard.edu
>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>>
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>> >>
>> >>
>> >> The 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 Partners Compliance
>> HelpLine at
>> >> http://www.partners.org/complianceline . If the e-mail was sent to
>> you
>> in error
>> >> but 

Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

[zkaufman]

Ah, I see. This issue must have arisen due to some changes I made in the
freesurfer git repository.

Eugenio, I should have this resolved by tomorrows build.

Alexandra, thanks for pointing this out. It should be fixed in tomorrows
daily build. Ill send you an email to confirm.

-Zeke


 Hi Zeke and Eugenio,

 Thanks for your quick answers.
 I removed the maverick distribution and installed the lion one pointed
 by Zeke.

 Running the segmentation, I get the same message as before:

 /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 35:
 /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
 No such file or directory

 Here is were the symbolic link is pointing:

 segmentSubjectT1_autoEstimateAlveusML -
 ../../../../../.git/annex/objects/gj/5f/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a

 It is pointing to a directory which is outside of freesurfer's.

 -Alexandra

 On 8/20/15 9:38 AM, Z K wrote:
 Hi Alexandra,

 The mavericks build that you downloaded was an experimental build that
 hasnt been updated for awhile. Please remove that version and download
 and install the lion version instead. That version is more up-to-date.
 Sorry for the confusion.

 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz


 -Zeke





 On 08/20/2015 04:42 AM, Eugenio Iglesias wrote:
 Hi Alexandra,
 that's weird. Where is the symbolic link pointing?
 Cheers,
 Eugenio

 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


 - Original Message -
 From: Alexandra De Araujo deara...@uoregon.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Thursday, August 20, 2015 1:45:02 AM
 Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6
 Beta -missing files?


 Hello,

 I have installed FreeSurfer v6
 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new
 hippocampal segmentation modules. I have installed it in my folder
 Application. Now, when I tried to run a hippocampal segmentation, I
 get the following error:

 /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 35:
 /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
 No such file or directory

 Looking into
 bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find
 segmentSubjectT1_autoEstimateAlveusML that looks like to be a
 symbolic link pointing to no existing file. I have similar problems
 when I try to run a T1T2 or a T2.

 Can someone help me with this issue?

 Thanks,

 Alex
 --
 Alexandra De Araujo
 Adjunct research assistant
 Brain and memory lab
 University of Oregon
 (+1) 541-346-6733
 --

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 the e-mail
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Re: [Freesurfer] Repost: problem with mri_label2label - large amount of holes

[zkaufman]

Hello Caspar,

I did a quick test and it appears the new dev version of mri_label2label
is still compatible with the version of 5.1 that you have. Please use the
following link to download it and also please make sure to back up the
version you already have.

  
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/mri_label2label

-Zeke


 Hi Bruce, Doug, and Zeke,
 just checking back regarding the dev version for mri_label2label.
 Do you have a build that works on  MAC OS 10.9.5 Mavericks?
 So far, we have been using
 freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.

 Thank you, Caspar


 2015-08-03 6:40 GMT-04:00 Caspar M. Schwiedrzik
 cschwie...@rockefeller.edu
 :

 We are using MAC OS 10.9.5 Mavericks and freesurfer-Darwin-leopard-
 i686-stable-pub-v5.1.0


 On Thursday, July 30, 2015, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:

 Hi Caspar

 the dev version of label2label doesn't have this problem. If you let us
 know your hardware/software environment Zeke can get you a new binary
 that
 should fix this issue

 cheers
 Bruce


 On Thu, 30 Jul 2015, Caspar M. Schwiedrzik wrote:

 Hi Bruce and Doug,
 thanks for looking into this and sorry for the delay.
 The command line we are using is:

 mri_label2label
 --srclabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p
 8.label --srcsubject y$1
 --trglabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp
 2.label --trgsubject yx$1 --regmethod surface --hemi lh

 We have several anatomies from the same subject, acquired on different
 occasions.
 We defined labels based on results of an fMRI experiment, and tried to
 use
 mri_label2label to map them within subjects from one anatomy to
 another.
 As a
 control, we also wanted to map the Hinds V1 from one anatomy to
 another,
 but this
 is where we ran into these holes.
 We will make an example subject available for debugging later today.

 Thanks! Caspar





 2015-07-24 12:33 GMT-04:00 Douglas Greve gr...@nmr.mgh.harvard.edu:
   what is your command line? What do you mean by one anatomy to
   another?

   On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote:


   -- Forwarded message --
   From: Caspar M. Schwiedrzik cschwie...@rockefeller.edu
   Date: Thursday, July 16, 2015
   Subject: problem with mri_label2label - large amount of holes
   To: Freesurfer@nmr.mgh.harvard.edu
   freesurfer@nmr.mgh.harvard.edu


   Hi!
 We are doing some analyses in which we map custom labels from one
 anatomy to another, within subjects. As a control, we also tried to
 map anatomically defined V1s according to the method by Hinds within
 subject from one anatomy to another. However, as you can see in the
 attachment, there are very many holes in the labels after using
 mri_label2label. This does not happen with smaller labels. Why is
 this happening and is there a solution?
 Thanks, Caspar







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 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
 in
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 but does not contain patient information, please contact the sender
 and
 properly
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Re: [Freesurfer] help

[zkaufman]

As the error message indicates, this is a permissions issue. To solve the
license problem, your best bet is to create the license files in your home
directory (or anywhere you have adequate permissions) and copy it to
/Applications/freesurfer. This is described in a little more detail in the
License section on this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac

Your subjects dir issue is essentially the same problem. The default
SUBJECTS_DIR (/Application/freesurfer/subjects) is write protected. So
either place the subject data somewhere you adequate permissions, and set
the SUBJECTS_DIR accordingly, or open up the permissions if the default
SUBJECTS_DIR using the following coomand:

$ sudo chmod -R a+w /Applications/freesurfer

Cheers,

-Zeke


 I am very new to Freesurfer and are having problems getting it up and
 running. I have followed, successfully the set up and configuration
 instructions up the license. At this point, after entering the license
 information received in the email I try and to exit and save and I get a
 message that reads   error writing license.txt: Permission Denied.



 However, we were able to run the Test your FreeSurfer Installation part
 successfully. But when we try to work with our own MRI scans, we receive a
 whole bunch of error message such as:



 mkdir: //Application/freesurfer/subjects/subj001: Permission denied



 I am guessing this is due to license.txt. How can I resolve this?

 Karen

 Karen Bunday, PhD
 Honorary Research Associate
 Sobell Department of Motor Neuroscience and Movement Disorders
 Institute of Neurology, University College London
 33 Queen Square
 London
 WC1N 3BG

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Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[zkaufman]

Hello,

Here is a download link to the most recent version of mri_tessellate:

ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_tessellate

Please place the new version in your $FREESURFER_HOME/bin directory, and
backup the original. Hope this helps.

-Zeke


 FREESURFER_HOME: /usr/local/freesurfer/stable5_3
 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
 Debian version: 7.6
 Kernel info: Linux 3.2.0-4-amd64 x86_64

 I think the info was at the end of the original email, as per
 instructions.

 I'm guessing it was just hidden, but let me know if there's any other info
 you need?

 Thanks!
 Ione


 -Original Message-
 From: freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
 Sent: Saturday, July 11, 2015 3:01 PM
 To: ionef...@uw.edu; Freesurfer support list
 Subject: Re: [Freesurfer] mri_tessellate: max vertices 100 exceeded

 Hi Iona

 if you tell us what your hardware/software environment is we'll get you a
 newer version.

 cheers
 Bruce
 On Sat, 11 Jul 2015, Ione Fine wrote:


 Hi,

 I am running to an error analyzing a 0.5 mm resolution T1 structural
 with the following with the following:

 recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT

  

 the issue seems to be:

 mri_tessellate: max vertices 100 exceeded

  

 There?s apparently a version of mri_tesselate which is easier going
 about the number of vertices, but the link to it is broken.

 https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/0400
 01.html

  

 Thanks

 Ione

  

 System information:

  

 FREESURFER_HOME: /usr/local/freesurfer/stable5_3

 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

 Debian version: 7.6

 Kernel info: Linux 3.2.0-4-amd64 x86_64

  

  

  

  

 Professor of Psychology

 University of Washington

 http://faculty.washington.edu/ionefine/

  

  





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Re: [Freesurfer] Segmentation fault in mris_fix_topology when compiling with gcc 4.8 + AVX2

[zkaufman]

I would be very interested on the data set (and exact command) you used
that exhibited a 25% speed up. Because our tests showed little to no
improvement in run time when using the -march=core-avx2 during compiling.

-Zeke


 Oh PS, AVX gives about 25% speed up compared to SSE. Would it be useful
 for me to send the data that it segfaults on?

 -Original Message-
 From: freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
 Sent: Tuesday, 23 June 2015 1:50 AM
 To: Freesurfer support list
 Subject: Re: [Freesurfer] Segmentation fault in mris_fix_topology when
 compiling with gcc 4.8 + AVX2

 Thank you for this information.

 -Zeke

 On 06/22/2015 02:22 AM, Chris Adamson wrote:
 Everyone,

 I know this is a fairly specific issue but nonetheless.

 If you compile Freesurfer 5.3.0 with the option -march=core-avx2 with
 gcc 4.8 it can cause mris_fix_topology to segfault at
 utils/mrisurf.c:64770 mrisCopyDefectPatch

 gcc 4.9 also does the same thing.

 If you still use AVX but disable AVX2, i.e. use -march=core-avx-i then
 it does not segfault.

 Just something to keep in mind.

 *Dr **Chris Adamson
 *Research Officer, Developmental Imaging, *Murdoch Childrens Research
 Institute *Murdoch Childrens Research Institute Royal Children's
 Hospital Flemington Road, Parkville, Victoria  3052, Australia
 www.mcri.edu.au http://www.mcri.edu.au/

 E   chris.adam...@mcri.edu.au
 T   03 9936 6780


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Re: [Freesurfer] freesurfer problem report

[zkaufman]

Hello Feng Liu,

What is the terminal output when you enter the following commands:

$ cd /media/sf_E_DRIVE/output/nv001/mri
$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
--i orig.mgz --o orig_nu.mgz

-Zeke

 Dear freesurfer experts,

 I came across a problem when I run freesurfer. I just download the
 freesurfer software ( VirtualboxXubuntu 12.04stable v5.3.015 Aug
 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G
 ). I install the software and configuration, and I changed subjects_dir as
 /media/sf_E_DRIVE. When I executed the command recon-all -s nv001 -all,
 there is error in the command window.

 The information of freesurfer problem are as follows:
 FREESURFER_HOME: /usr/local/freesurfer

 Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

 Debian version: wheezy/sid

 Kernel info: Linux 3.2.0-23-generic i686

 -
 Please include the following additional information in your report:

   1) subject name
 nv001
   2) the entire command-line executed
 recon-all -s nv001 -all
   3) the error message generated
 INFO: extension is mgz
 #
 #@# Talairach Sun Jun 14 12:25:31 EDT 2015
 /media/sf_E_DRIVE/output/nv001/mri

  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
 --i orig.mgz --o orig_nu.mgz

 Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

 recon-all -s nv001 -all exited with ERRORS at Sun Jun 14 12:25:42 EDT
 2015

 For more details, see the log file
 /media/sf_E_DRIVE/output/nv001/scripts/recon-all.log
 To report a problem, see
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
   4) optionally include the subject's /script/recon-all.log
 Attached

 However, if I am not change the subjects_dir (usr the default:
 /usr/local/freesurfer/subjects), there is no error information.

 I do not know where I am wrong.
 Would greatly appreciate any form of help!

 2015-06-15



 Feng Liu, Ph.D.
 Department of Radiology,
 Tianjin Medical University General Hospital,
 No. 154, Anshan Road, Heping District, Tianjin
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Re: [Freesurfer] TKMEDIT error when SSH'ing

[zkaufman]

Have you verified that the machine you are ssh'ing into will display
tkmedit even if you are not ssh'ing into it? I ask because OSX 10.6 is an
end-of-life operating system and that error is usually associated with
incompatible graphics card.

However, even if it did work while sitting at the host machine, I have
never been able to successfully perform X Forwarding over ssh from one Mac
to another Mac when using the tktools, or any graphical tools that I can
recall for that matter.

-Zeke


 Hi Freesurfer folks

 I am SSH'ing from one MAC to another.  both mac's are running Mac Os
 10.6.8

 I am  ssh'ing with  -Y option

 when I try to run tkmedit I get the error;


 Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error:
 kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 2763
 Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error:
 kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as
 they are logged.
 Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error:
 kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0xacb
 Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error: unknown
 error code: invalid drawable
 error: xp_attach_gl_context returned: 2
 X Error of failed request:  0
   Major opcode of failed request:  150 (GLX)
   Minor opcode of failed request:  26 (X_GLXMakeContextCurrent)
   Serial number of failed request:  24
   Current serial number in output stream:  24

 How can I fix this?

 Jon




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Re: [Freesurfer] Upgrading Software

[zkaufman]

 Hello,


 Is there any detailed information on the possible differences in results
 wwhen upgrading to the latest FreeSurfer software?

 As it pertains to the scans already processed with old software compared
 to
 any scans processed with a newer version of the software.

When freesurfer6.0 is released we will publish a set of brain maps for
some of our internal data sets which will show the regions of the brain
that demonstrate statistical differences for various measures (e.g.
thickness, area) between the most recent release v5.3 and the upcoming
release v6.0. Whether your data will exhibit the same trends is impossible
to say. But we do make the following statement on our download page in
regards to processing subjects with freesurfer:



*Important Note!* When processing a group of subjects for your study, it
is essential to process all your subjects with the same version of
freesurfer, on the same OS platform and vendor, and for safety, even the
same version of the OS. While we continue to work to ensure that results
match across platforms (for instance the 32b and 64b CentOS 4 builds
should produce identical results), there are none-the-less system-level
libraries that are OS dependent. An exception to this rule is that you may
view and edit files across any platform or version, and run some
post-processing tools (outside the recon-all stream) if you check with us
first (for instance you may run the longitudinal processing with newer
versions).



 Can I install the new version of Freeview without the new version of
 FreeSurfer? Would there be any differences to between scans corrected
 before and after upgrade?

Yes, you can install the new version of freeview over your existing
version of freeview as updates to that application, and edits made with
it, should not effect to overall processing stream. Just follow the
Freeview dev version download instructions on this page:

https://surfer.nmr.mgh.harvard.edu/fswiki/Download

 I cannot seem to get the 'curl -O' to download the software. Are there any
 troubleshooting methods to this? Testing the harvard ftp server also
 fails.
 Has it been down?

I just tested the following commands on my home network and they both
worked for me.

$ curl -O
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg

$ curl -O
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/lion/Freeview.zip


-Zeke


 Thank you so much,

 Joseph
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Re: [Freesurfer] Freeview mountain lion

[zkaufman]

Hello Isabelle,

Freeview has been undergoing many changes and you simply got unlucky and
downloaded an unstable version of the program. I will be posting an
updated version within the day and I will email you directly when it
becomes available.

-Zeke

 htmlheadmeta http-equiv=Content-Type content=text/html
 charset=us-ascii/headbody style=word-wrap: break-word;
 -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; Hi
 there,divbr/divdivI recently tried to update the Freeview version
 so I can have the recon edit button. I managed to copy the file over but
 now I get the following error:/divdivbr/divdivdivdyld: Library
 not loaded:
 @executable_path/../Frameworks/QtScriptTools.framework/Versions/4/QtScriptTools/divdivnbsp;
 Referenced from:
 /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview/divdivnbsp;
 Reason: image not found/divdivTrace/BPT
 trap/div/divdivbr/divdivWhen I double click on the Freeveiw
 app I get a more detailed error:/divdivbr/divdivdivProcess:
 nbsp; nbsp; nbsp; nbsp; Freeview [10010]/divdivPath: nbsp; nbsp;
 nbsp; nbsp; nbsp;
 nbsp;/Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview/divdivIdentifier:
 nbsp; nbsp; nbsp;Freeview/divdivVersion: nbsp; nbsp; nbsp;
 nbsp; ???/divdivCode Type: nbsp; nbsp; nbsp; X86-64
 (Native)/divdivParent Process: nbsp;tcsh [10008]/divdivUser ID:
 nbsp; nbsp; nbsp; nbsp; 501/divdivbr/divdivDate/Time: nbsp;
 nbsp; nbsp; 2015-05-14 08:33:50.177 -0400/divdivOS Version: nbsp;
 nbsp; nbsp;Mac OS X 10.8.5 (12F2518)/divdivReport Version:
 nbsp;10/divdivbr/divdivInterval Since Last Report: nbsp;
 nbsp; nbsp; nbsp; nbsp;858 sec/divdivCrashes Since Last Report:
 nbsp; nbsp; nbsp; nbsp; nbsp; 2/divdivPer-App Crashes Since Last
 Report: nbsp; 2/divdivAnonymous UUID: nbsp; nbsp; nbsp; nbsp;
 nbsp; nbsp; nbsp; nbsp; nbsp; nbsp;
 nbsp;83D92F1C-F624-48C3-3831-9BD909D04175/divdivbr/divdivCrashed
 Thread: nbsp;0/divdivbr/divdivException Type:
 nbsp;EXC_BREAKPOINT (SIGTRAP)/divdivException Codes:
 0x0002,
 0x/divdivbr/divdivApplication Specific
 Information:/divdivdyld: launch, loading dependent
 libraries/divdivbr/divdivDyld Error Message:/divdivnbsp;
 Library not loaded:
 @executable_path/../Frameworks/QtScriptTools.framework/Versions/4/QtScriptTools/divdivnbsp;
 Referenced from:
 /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview/divdivnbsp;
 Reason: image not found/divdivbr/divdivBinary
 Images:/divdivnbsp; nbsp; nbsp; nbsp;0x1046ba000 - nbsp; nbsp;
 nbsp; nbsp;0x105d9efe7 +com.yourcompany.Freeview (???)
 lt;B8372BB3-6D84-3476-801A-B559A19B6C05gt;
 /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview/divdivnbsp;
 nbsp; nbsp; nbsp;0x106c8a000 - nbsp; nbsp; nbsp; nbsp;0x106c94ff7
 +libgomp.1.dylib (2) lt;33BB1457-AC5A-343C-B6FA-F70EEC21BF69gt;
 /Users/USER/*/libgomp.1.dylib/divdivnbsp; nbsp; nbsp;
 nbsp;0x106ca6000 - nbsp; nbsp; nbsp; nbsp;0x106efdfe7 +QtScript
 (4.7.4) lt;22C41B2A-3C52-B7E9-37A8-EF71E48EE9FBgt;
 /Applications/freesurfer/Freeview.app/Contents/Frameworks/QtScript.framework/Versions/4/QtScript/divdivnbsp;
 nbsp; nbsp; nbsp;0x106f56000 - nbsp; nbsp; nbsp; nbsp;0x1071deff7
 +QtCore (4.7.4) lt;9EB52EC3-3C0F-0A45-1CE6-227EB7069767gt;
 /Applications/freesurfer/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/4/QtCore/divdivnbsp;
 nbsp; 0x7fff642ba000 - nbsp; nbsp; 0x7fff642ee94f nbsp;dyld (210.2.3)
 lt;8958FE97-5830-3928-BC38-23136E7D3783gt;
 /usr/lib/dyld/divdivnbsp; nbsp; 0x7fff8e6be000 - nbsp; nbsp;
 0x7fff8e6befff nbsp;com.apple.Cocoa (6.7 - 19)
 lt;1F77945C-F37A-3171-B22E-F7AB0FCBB4D4gt;
 /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa/divdivnbsp;
 nbsp; 0x7fff8eb63000 - nbsp; nbsp; 0x7fff8ebd1fff
 nbsp;com.apple.framework.IOKit (2.0.1 - 755.42.2)
 lt;18E64CC5-2671-3C47-B2C6-0EEEDF899461gt;
 /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit/divdivnbsp;
 nbsp; 0x7fff8f5e1000 - nbsp; nbsp; 0x7fff8f5e1fff
 nbsp;com.apple.Accelerate (1.8 - Accelerate 1.8)
 lt;878A6E7E-CB34-380F-8212-47FBF12C7C96gt;
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate/divdivbr/divdivModel:
 MacBookPro9,2, BootROM MBP91.00D3.B09, 2 processors, Intel Core i7, 2.9
 GHz, 8 GB, SMC 2.2f44/divdivGraphics: Intel HD Graphics 4000, Intel HD
 Graphics 4000, Built-In, 512 MB/divdivMemory Module: BANK 0/DIMM0, 4
 GB, DDR3, 1600 MHz, 0x02FE,
 0x45424A3431554638424455352D474E2D4620/divdivMemory Module: BANK
 1/DIMM0, 4 GB, DDR3, 1600 MHz, 0x02FE,
 0x45424A3431554638424455352D474E2D4620/divdivAirPort:
 spairport_wireless_card_type_airport_extreme (0x14E4, 0xF5), Broadcom
 BCM43xx 1.0 (5.106.98.100.17)/divdivBluetooth: Version 4.1.7f5 15113,
 3 service, 21 devices, 3 incoming serial ports/divdivNetwork Service:
 Ethernet, Ethernet, en0/divdivSerial ATA Device: APPLE HDD
 HTS541010A9E662, 1 TB/divdivSerial ATA Device: MATSHITADVD-R nbsp;
 UJ-8A8/divdivUSB Device: hub_device, 0x8087 nbsp;(Intel Corporation),
 0x0024, 0x1a10 / 2/divdivUSB Device: FaceTime HD Camera

Re: [Freesurfer] kvlThresholImage fails on MacOSX 10.10.2

[zkaufman]

Can you please provide me with the Processor and Graphics hardware
specs of the machine listed under Apple - About This Mac.

Ive only ever seen this error on old mac minis and its usually indicative
of an incompatible graphics card.

 Dear freesurfer,

 I tried using kvlThresholdImage on a MacOSX 10.10.2, X version XQuartz
 2.7.7 (xorg-server 1.15.2), and freesurfer version 5.3, and I get the
 following message:

 kvlThresholdImage subj01/mri/orig/orig.mgz

 0

 2370

 X Error of failed request:  BadWindow (invalid Window parameter)

   Major opcode of failed request:  2 (X_ChangeWindowAttributes)

   Resource id in failed request:  0x33d23c0

   Serial number of failed request:  7

   Current serial number in output stream:  9


 Do you have any solution for this error? Or any suggestions?

 Many thanks for your great work!


 Dr. Fabio Dalpra
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Re: [Freesurfer] -openmp 8 and -use-gpu questions

[zkaufman]

 I'm testing the total processing time of recon-all -all using -openmp
 4,6,8,12 .
 The runs with 4 and 6 threads took almost the same amount of time.
 The runs with 8 and 12 threads took almost the same amount of time.

 (1)Is the work divided evenly between the threads (mri_ca_register,
 mri_en_register)?   Or is 4 or 8 preferred and 6 and 12 don't buy you
 anything?


I can verify that the gain in processing time due to additional threads
falls off rapidly with very little gain after 4. I dont know the exact
times you got from your tests, and I havent done a time analysis in
awhile, but we've never noticed a correlation preferring 4 and 8 threads
over 6 and 12. However its an interesting result and could very well be
the case.


 (2)Is there a sync point in the software so that all the other
 threads wait for the slowest one to complete.


I dont do much of the openmp programming within freesurfer (only for
debugging purposes) but as far as I can tell all the openmp relevant code
blocks occur at for-loop where threads are all created and diverge
simultaneously and then sync and at the same time at the conclusion of the
for-loop.

If you have an 8-12 processor machine and are looking to reduce your
runtimes you can take advantage of the fact that the left and right
hemispheres can be processed independently during the autorecon2 stage.
You could write a custom script along the lines of:

  recon-all -s subj -autorecon1
  recon-all -s subj -autorecon2-volonly
  recon-all -s subj -autorecon2-perhemi -hemi rh -log recon-all-hemi
rh.log -notify rh-done.log -openmp 4 
  recon-all -s subj -autorecon2-perhemi -hemi lh -log
recon-all-hemi-lh.log -notify lh-done.log -openmp 4 
  while (rh-done.log AND lh-done.log do not both exist)
  do
sleep 1
  end loop
  recon-all -s -autorecon3


 Also, I tried a run with -use-gpu.
 I had to add a directory to LD_LIBRARY_PATH or I get an error on failure
 to find one of the libcuda's
 That is now ok but I get the following:

 Testing for CUDA device:
 ERROR: Unable to acquire a CUDA device!
 nvcc: NVIDIA (R) Cuda compiler driver
 Copyright (c) 2005-2012 NVIDIA Corporation
 Built on Fri_Sep_21_17:28:58_PDT_2012
 Cuda compilation tools, release 5.0, V0.2.1221

 Acquiring CUDA device
 Using default device
 Linux comet-30-08.sdsc.edu 3.10.73-1.el6.elrepo.x86_64 #1 SMP Thu Mar 26
 16:28:30 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux

 recon-all -s 173_1gpu exited with ERRORS at Thu Apr 30 09:17:42 PDT
 2015_PATH  but then I get the following error:

 Any thoughts would be welcome.

 Thanks,



Sorry but weve completely abandoned all support of CUDA in favor of
openmp. That said, people successfully have and still do use cuda with
freesurfer v5.3. Assuming you have a cuda device compatible with the cuda
libs shipped with freesurfer it should simply work without you having to
modify LD_LIBRARY_PATH, but perhaps someone who has had success in this
relm can chime in.

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Re: [Freesurfer] hello freesurfer developer~

[zkaufman]

A-reum,

Opening jpeg compressed dicoms is new feature so please bear with us as we
try and get this working for you. Use the link below to download the
libdcmjpeg.so.3.6.0 file.

ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/libdcmjpeg.so.3.6

Once the download is complete, please copy the file into your
$FREESURFER_HOME/lib folder. Additionally, you will need to type the
following command into your terminal window AFTER you load freesurfer.

(If you are using bash)
export LD_LIBRARY_PATH=$FREESURFER_HOME/lib

(Or, if you are using csh)
setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib

Please let us know if this solves the issue.

-Zeke






 Hi doug

 dcmdjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin)

 I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and
 then show up these

 dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6:
 cannot open shared object file: No such file or directory

 always error in tmp file(x signed root.tmp.decompressed.dcm.000).

 so, fix the x signed root.tmp.decompressed files... and i have no
 libdcmjpeg.so.3.6.. i need it.

 2015-04-03 12:39 GMT+09:00 A-reum Min naniy...@gmail.com:

 Hi doug

 dcmdjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin)

 I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and
 then show up these

 dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6:
 cannot open shared object file: No such file or directory

 always error in tmp file(x signed root.tmp.decompressed.dcm.000).

 so, fix the x signed root.tmp.decompressed files... and i have no
 libdcmjpeg.so.3.6.. i need it.



 2015-04-03 7:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:

 Is dcmdjpeg.fs in your path? What are the contents of the file
 /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ?


 On 04/02/2015 04:53 PM, A-reum Min wrote:
  Hi doug.
  I try this as a test.
  (here is a my terminal)
 
 ***
  [areum@localhost ~]$ su
  Password:
  [root@localhost areum]# tcsh
  [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer
  [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh
   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
  Setting up environment for FreeSurfer/FS-FAST (and FSL)
  FREESURFER_HOME   /usr/local/freesurfer
  FSFAST_HOME   /usr/local/freesurfer/fsfast
  FSF_OUTPUT_FORMAT nii.gz
  SUBJECTS_DIR  /usr/local/freesurfer/subjects
  MNI_DIR   /usr/local/freesurfer/mni
  [areum@localhost areum]# setenv SUBJECTS_DIR
  /usr/local/freesurfer/subjects/PISA_SPGR/1
  [areum@localhost areum]# setenv FS_LOAD_DWI 0
  [areum@localhost areum]# mri_convert
  /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh
  mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
  junk.mgh
  $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $
  reading from
 /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm...
  Starting DICOMRead2()
  dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
  dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1
  Ref Series No = 3
  Found 246 files, checking for dicoms
  Found 244 dicom files in series.
  First Sorting
  Computing Slice Direction
  Vs: -0.8 0 0
  Vs: -1 0 0
  Second Sorting
  Counting frames
  nframes = 1
  nslices = 244
  ndcmfiles = 244
  IsDWI = 0
  PE Dir = ROW (dicom read)
  Loading pixel data
  JPEG compressed, decompressing
  cd /home/areum
  dcmdjpeg.fs +te
  /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
  /tmp/root.tmp.decompressed.dcm.QGcfri 
  /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out
  ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out
  for more details
 
 **
  error occured again.. ㅜㅜ
  when i type the  source $FREESURFER_HOME/SetUpFreeSurfer.csh, then
  show up these
   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
  Setting up environment for FreeSurfer/FS-FAST (and FSL)
  FREESURFER_HOME   /usr/local/freesurfer
  FSFAST_HOME   /usr/local/freesurfer/fsfast
  FSF_OUTPUT_FORMAT nii.gz
  SUBJECTS_DIR  /usr/local/freesurfer/subjects
  MNI_DIR   /usr/local/freesurfer/mni
  But... my own data directory is
 /usr/local/freesurfer/subjects/PISA_SPGR/1
  so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1
  is it okay...?
  and i will send my dicom file to u... plz help me as soon as possible
 ㅜㅜ
  2015-04-03 5:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu:
 
  Can you send me
  /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm
  ? I might not be able to get to it until after the 13th.
 
  Also, try 

Re: [Freesurfer] hello freesurfer developer~

[zkaufman]

A-reum,

Please download the following file:

ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/dcmdjpeg.fs

And replace your existing $FREESURFER_HOME/bin/dcmdjpeg.fs file with the
one from the link above. Also, make sure it is set to executable by typing
the following in a terminal window:

$ chmod a+x $FREESURFER_HOME/bin/dcmdjpeg.fs

And then try again.

-Zeke


 Hi doug... recon-all dosen't working..

 If i type the recon-all -i~
 then, error occured...

 +

 JPEG compressed, decompressing
 cd /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01
 dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_FSPGR/1/I0071579.dcm
 /tmp/root.tmp.decompressed.dcm.kBIYHL 
 /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out
 ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out for
 more details
 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15
 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

 recon-all -s subj01 exited with ERRORS at Fri Apr  3 10:39:27 PDT 2015

 For more details, see the log file
 /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01/scripts/recon-all.log
 To report a problem, see
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

 ++

 I copy the libdcmjpeg.so.3.6 and paste in FREESURFER_HOME/lib
 after that type the setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib

 but.. didn't working ..

 same error occured -- dcmdjpeg.fs: error while loading shared libraries:
 libdcmjpeg.so.3.6: cannot open shared object file: No such file or
 directory

 and i click the root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out then show up
 these

 dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6:
 cannot open shared object file: No such file or directory

 how can i to do ㅜㅜ help me doug
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Re: [Freesurfer] Trac-all error

[zkaufman]

Hello Emad,

The download page states that OSX versions of freesurfer require the user
to download and install XQuartz onto their machine. I have updated the
download page so it is a little more clear.
https://surfer.nmr.mgh.harvard.edu/fswiki/Download

Also, the dev version of freesurfer is in a high degree of flux right now.
We are undergoing compiler upgrades and other various changes to the
build. This means I would expect the nightly builds to be unstable for the
next couple days.

But installing XQuartz should resolve the issue you experienced below.

-Zeke



 Hello Anastasia,

 I’m using the nightly-built version for Mac OS Lion; I double checked it
 by the command freesurfer -ver and got this response:

 You are running this version of FreeSurfer:

   freesurfer-Darwin-lion-dev-20150227

 I’m using this version on Mac OS X Yosemite. I tried to re-download a
 nightly built version, but it didn’t let me (presumably because it’s
 workshop time). Please let me know how I should proceed.

 Yours,
 Emad

 On Mar 6, 2015, at 7:11 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:


 Hi Emad - The error is:
  dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib

 Does the freesurfer build that you're using match the computer that
 you're running it on?

 a.y

 On Wed, 4 Mar 2015, Emad Ahmadi wrote:

 Hello Freesurfers!

 I’m trying to use tracheal -prep, and I’m getting an error. Would
 you please help me with figuring out where the problem is? The log file
 is attached.

 Thank you very much,
 Emad



 Emad Ahmadi, MD
 ---
 Research Fellow
 Department of Radiology
 Massachusetts General Hospital
 Harvard Medical School

 25 New Chardon Street, Suite 400
 Boston, MA 02114
 Tel: 617 726 5237
 Email: e...@nmr.mgh.harvard.edu

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Re: [Freesurfer] regarding license.txt file

[zkaufman]

The freesurfer installation does NOT contain a license file. You must
create it, first by creating a file called license.txt in your
FREESURFER_HOME directory, then copy/paste the contents specified in the
email you recieved into the license.txt file.

-Zeke


 Hi,

 I downloaded the latest version of the freesurfer and tried to install it.
 After running the installation, I registered my information in
 https://surfer.nmr.mgh.harvard.edu/registration.html

 I received an email after few minutes with an information that I have to
 replace a text inside the license.txt file. So, I went back and try to do
 that. But I cannot locate the license.txt file. It does contain LICENSE
 file but doesn't have an information that I need to replace.

 Later, I went back and download the latest version of freesurfer again
 thinking I may have made a mistake at first installation but even the
 later installation didn't contain any license.txt file.

 The freesurfer that I download was from
 https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#Download

 The detail of the file is below
 Linux

 CentOS 6 x86_64 (64b)

 stable v5.3.0

 15 May 2013

 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gzftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

 4.2G


 Thank you for you time.

 Regards,

 Prabesh?

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Re: [Freesurfer] Freesurfer Version

[zkaufman]

The 64bit Lion version. It should probably be made a little more clear
that that version is for 10.7 and higher. Ill fix that.

https://surfer.nmr.mgh.harvard.edu/fswiki/Download

-Zeke


 Gentleman
 Which Version of Freesurfer should I download for use with the OS X
 Yosemite 10.10.1?
 Thanks
 Cristian
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Re: [Freesurfer] permission denied

[zkaufman]

Yes, please try running as root and get back when you have the chance.
This is a very odd issue and your results when running as root will
provide insight.

-Zeke

 Hi Z K,

 Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one
 installed with the latest freesurfer version did not work while others
 finished the processing in a reasonable processing time and I got the
 results.

 Also, I have a PC at my office installed with the latest freesurfer
 version
 and it works fine. So I have two PCs installed with the latest Freesurfer
 (one of them which does not work is in the lab).


 To summarize:
 All PCs (16 PCs in the lab and 1 in my office) are installed with latest
 Ubuntu version 14.04 64 bits
 15 PCs in the lab are installed with freesurfer 5.0.0 version
 1 PC in the lab is installed with the latest freesurfer version (does not
 work, permission denied)
 1 PC in my office is installed with the latest freesurfer version (works
 fine)

 All these PCs have Ubuntu 14.04 64bit installed on them.



 No, I am not using any vitual machine.

 Regarding the root user, I will try it on Sunday as I am away for a couple
 of days.

 Many thanks for your continuous support.

 Ali




 On Thu, Oct 30, 2014 at 6:34 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:

 Ali,

 First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are
 working properly? I am under the impression that versions of freesurfer
 pre-version 5.3 will not work on newer linux distributions?


 In regards to your current permision denied issue... What happens if you
 try and run tkmedit as root user? Also, you not using virtual machine
 setup are you?

 -Zeke

 On 10/30/2014 06:27 AM, Ali Radaideh wrote:
  It does not work. This is really strange
 
  On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu
  mailto:zkauf...@nmr.mgh.harvard.edu wrote:
 
  I beleive it should have a lower case X, as in:
 
  chmod -R a+x freesurfer/bin
 
  -Zeke
 
  On 10/28/2014 01:19 AM, Ali Radaideh wrote:
Dear Douglas
   
Thanks for your reply. unfortunatey I still get the same error.
  Here is
the terminal output. Is there anything else I can do?
   
 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl
imaging@imaging-ThinkCentre-23:~$ tcsh
imaging-ThinkCentre-23:~ tkmedit
/usr/local/freesurfer/bin/tkmedit: Permission denied.
imaging-ThinkCentre-23:~
   
   
On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu wrote:
   
   
Try chmod -R a+X freesurfer/bin
   
   
On 10/26/14 1:57 PM, Ali Radaideh wrote:
Dear FreeSurfer users,
   
I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One
  of the
PCs has the latest version of freesurfer 5.3.0 while the
 others
have the version 5.0.0. The PC that is installed with the
 latest
version freesurfer 5.3.0 does not allow me to run any
  command and
everytime I try a command such such as tkmedit i get the
  following
error
/usr/local/freesurfer/bin/tkmedit: permission denied.
   
I have tried to change the permission settings
sudo chown -R imaging:imaging freesurfer
   
but did not work.
   
Any ideas why is this happening although I have done the
 same
thing to other PCs and they are working fine.
   
​Thanks in advance,
Ali​
   
--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo
  mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  mailto:ali.radai...@hu.edu.jo
/
/webpage:
 http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
   
   
   
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Re: [Freesurfer] segmentation fault mri_convert Ubuntu 14.04

[zkaufman]

Hello Alessandra,

This is a known issue with pre-freesurfer v5.3 releases and the most
recent version of Ubuntu. To fix the issue, if you have access to a
machine that still runs Ubuntu 12.04, please do the following:

  1) On the Ubuntu 12.04 system, find the find the file libcrypt-2.*.so
usually located in the /lib64 folder. (/lib/i386-linux-gnu on 32bit
machines).

  2) Copy that file into the $FREESURFER_HOME/lib on your new Ubuntu 14.04
machine and give it the name libcrypt.so.1.

  3) Lastly, after loading freesurfer, update your LD_LIBRARY_PATH
environment variable to include the $FREESURFER_HOME/lib directory. This
can either be done manually in the terminal or in your .cshrc file (or
.bashrc file).

  $ setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib:$LD_LIBRARY_PATH

Hope this helps. Contact me directly if you have a any specific issues. Also,
if you are unable to find a version of libcrypt on an older version of
Ubuntu let me know and I will search for one.

-Zeke






 Dear all,

 I am running FreeSurfer version [recon-all,v 1.313.2.6 2010/08/04] on an
 Ubuntu machine.
 After updating my system from Ubuntu 12.04 to Ubuntu 14.04 I get a
 segmentation fault when I try to resample images using mri_convert:

 /mri_convert -vs 1 1 1 /folder/original_image.nii.gz /folder/resampled
 image.nii.gz //
 //$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $//
 //reading from /folder/original_image.nii.gz...//
 //Segmentation fault (core dumped)/

 Any help on this?
 (for consistency with an on-going study I would like not to install a
 newer FreeSurfer version)

 Thank you very much!
 Alessandra


 --
 --
 Alessandra Griffa
 Doctoral assistant

 Signal Processing Laboratory 5
 EPFL STI IEL LTS5
 ELD 233 (Bâtiment ELD)
 Station 11 CH-1015
 Lausanne
 Tel.: +41216934807

 web: http://lts5www.epfl.ch/
 personal page: http://people.epfl.ch/alessandra.griffa?lang=en
 --

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Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

[zkaufman]

 Bruce,

 By symlink from your /mnt/hgfs/mydata/fsaverage to
 /usr/local/freesurfer/subjects/fsaverage you mean ln -s
 /mnt/hgfs/mydata/fsaverage  /usr/local/freesurfer/subjects/fsaverage ?
 which fsaverage is the target ?

 Thanks,
 Mahmoud


The target fsaverage is the one that came with the installation. Which
you no longer have so I have created a link for you to download it again
and put it back in your $SUBJECTS_DIR (see next answer).


 On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud zeydab...@gmail.com wrote:

 Bruce,

 Thank you for your follow up and advice. Please let me know:
 1- How to download the fsaverage again?

Ive created a link for you to download it:
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/Linux_centos4_x86_64/fsaverage.tar.gz

 2- should I do the symlink manually or it will be done by recon-all
 later ?

Just extract the file above into your $SUBJECTS_DIR so that you have a
$SUBJECTS_DIR/fsaverage directory and recon-all will take care of the
rest.

 3- What steps should I take before running the recon-all -all ? should I
 create any specific directory? set any permission ?

None. Hopefully this will just work.


-Zeke
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Re: [Freesurfer] CORRECTION ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

[zkaufman]

Here is the proper link.

ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/fsaverage.tar.gz


 Bruce,

 By symlink from your /mnt/hgfs/mydata/fsaverage to
 /usr/local/freesurfer/subjects/fsaverage you mean ln -s
 /mnt/hgfs/mydata/fsaverage  /usr/local/freesurfer/subjects/fsaverage ?
 which fsaverage is the target ?

 Thanks,
 Mahmoud


 The target fsaverage is the one that came with the installation. Which
 you no longer have so I have created a link for you to download it again
 and put it back in your $SUBJECTS_DIR (see next answer).


 On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud zeydab...@gmail.com wrote:

 Bruce,

 Thank you for your follow up and advice. Please let me know:
 1- How to download the fsaverage again?

 Ive created a link for you to download it:
 ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/Linux_centos4_x86_64/fsaverage.tar.gz

 2- should I do the symlink manually or it will be done by recon-all
 later ?

 Just extract the file above into your $SUBJECTS_DIR so that you have a
 $SUBJECTS_DIR/fsaverage directory and recon-all will take care of the
 rest.

 3- What steps should I take before running the recon-all -all ? should
 I
 create any specific directory? set any permission ?

 None. Hopefully this will just work.


 -Zeke
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Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

[zkaufman]

Mahmoud,

If I recall correctly, your on a virtual machine with the /mnt/hgfs/mydata
directory being a shared directory, and you werent able to write to it
when running recon-all.

So, what you want to do is create another directory within your virtual
machine that holds your subjects data. You will still need the
$FREESURFER_HOME/subjects directory because that directory contains files
required by recon-all, so you will have a separate directory which
contains your subjects.

You should not be creating symlinks or anything like that.

Just restore the fsaverage directory from the link I sent you back into
$FREESURFER_HOME/subjects, put your subject data somewhere else in the VM,
and run recon-all with the correct arguments.

-Zeke


 yes, that is true. If it's already there the symlink will fail. You
 should be able to rm it if it is there an incorrect (or leave it if it is
 there and correct)
 On Fri, 19 Sep 2014, Mahmoud wrote:

 Bruce and Zeke,
 Thank you so much for your advice.
 The last question before running the recon again. if I say:
 cd  /mnt/hgfs/mydata
 ln -s /usr/local/freesurfer/subjects/fsaverage

 It means that I shouldn't already have the fsaverage under /mydata
 directory, right ?

 Mahmoud

 On Fri, Sep 19, 2014 at 12:09 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu
 wrote:
   the easiest thing to do is:

   cd  /mnt/hgfs/mydata
   ln -s /usr/local/freesurfer/subjects/fsaverage


   then you don't have to worry about source and target. It will
   implicitly create the symlink in $PWD

   cheers
   Bruce
   On Fri, 19 Sep 2014, Mahmoud wrote:

 Bruce,

 By symlink from your /mnt/hgfs/mydata/fsaverage to
 /usr/local/freesurfer/subjects/fsaverage you mean
 ln -s
 /mnt/hgfs/mydata/fsaverage 
 /usr/local/freesurfer/subjects/fsaverage ?
 which fsaverage is the target ?

 Thanks,
 Mahmoud

 On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud
 zeydab...@gmail.com wrote:
       Bruce,
 Thank you for your follow up and advice. Please let
 me know:
 1- How to download the fsaverage again?
 2- should I do the symlink manually or it will be
 done by recon-all
 later ?
 3- What steps should I take before running the
 recon-all -all ? should
 I create any specific directory? set any permission
 ?

 Best,
 Mahmoud

 On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu wrote:
       yes, you symlinked it to itself which is why
 you are
       getting the infinite recursion error. You need
 to delete
       /usr/local/freesurfer/subjects/fsaverage

       and download the fsaverage dir again, put it
 in that
       directory, then symlink from your
       /mnt/hgfs/mydata/fsaverage to
       /usr/local/freesurfer/subjects/fsaverage

       cheers
       Bruce
       On Fri, 19 Sep 2014, Mahmoud wrote:

             Bruce,

             I already had my data in a shared folder
             (/mnt/hgfs/mydata) but I got the
             permission error the same point that I
 got the
             symlink error lastly. So, I
             tought that might be due to something
 related
             to shared directory.
             Then I copied my subjects under the
             $SUBJECTS_DIR but got the symlink error.

             running ls -l
 /usr/local/freesurfer/subjects
             /fsaverage  shows me this:

             lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18
 20:23
             /usr/local/freesurfer/subjects/fsaverage
 -
             /usr/local/freesurfer/subjects/fsaverage

             Thank you,
             Mahmoud


             On Fri, Sep 19, 2014 at 9:23 AM, Bruce
 Fischl
             fis...@nmr.mgh.harvard.edu
             wrote:
                   the  directory
             /usr/local/freesurfer/subjects is for
 subjects
                   that we distribute and NOT where
 you
             should be putting your
                   subject data. Is that what you
 are
             doing? You may have

Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

[zkaufman]

I believe if you simply run:

$ recon-all -i /volumetric/Case018/case018_tp2/22-1.dcm -subject
case018_tp2 -all

You should be all set. You do not need to type any of the following commands:

 clear
 cd  /volumetric
 ln -s /usr/local/freesurfer/subjects/fsaverage


-Zeke



 Zeke,

 I created another directory named volumetric and put my data under it.
 To final check before running the recon-all, here is the info from
 terminal:
  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 FREESURFER_HOME   /usr/local/freesurfer
 FSFAST_HOME   /usr/local/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii.gz
 SUBJECTS_DIR  /usr/local/freesurfer/subjects
 MNI_DIR   /usr/local/freesurfer/mni
 ubuntu:~ cd /volumetric
 ubuntu:/volumetric ls
 Case018  Case022


 and I'm going to run this:

 #!/bin/tcsh

 clear
 cd  /volumetric
 ln -s /usr/local/freesurfer/subjects/fsaverage

 recon-all -i /volumetric/Case018/case018_tp2/22-1.dcm -subject
 case018_tp2
 -all

 On Fri, Sep 19, 2014 at 1:24 PM, zkauf...@nmr.mgh.harvard.edu wrote:

 Mahmoud,

 If I recall correctly, your on a virtual machine with the
 /mnt/hgfs/mydata
 directory being a shared directory, and you werent able to write to it
 when running recon-all.

 So, what you want to do is create another directory within your virtual
 machine that holds your subjects data. You will still need the
 $FREESURFER_HOME/subjects directory because that directory contains
 files
 required by recon-all, so you will have a separate directory which
 contains your subjects.

 You should not be creating symlinks or anything like that.

 Just restore the fsaverage directory from the link I sent you back into
 $FREESURFER_HOME/subjects, put your subject data somewhere else in the
 VM,
 and run recon-all with the correct arguments.

 -Zeke


  yes, that is true. If it's already there the symlink will fail. You
  should be able to rm it if it is there an incorrect (or leave it if it
 is
  there and correct)
  On Fri, 19 Sep 2014, Mahmoud wrote:
 
  Bruce and Zeke,
  Thank you so much for your advice.
  The last question before running the recon again. if I say:
  cd  /mnt/hgfs/mydata
  ln -s /usr/local/freesurfer/subjects/fsaverage
 
  It means that I shouldn't already have the fsaverage under /mydata
  directory, right ?
 
  Mahmoud
 
  On Fri, Sep 19, 2014 at 12:09 PM, Bruce Fischl
  fis...@nmr.mgh.harvard.edu
  wrote:
the easiest thing to do is:
 
cd  /mnt/hgfs/mydata
ln -s /usr/local/freesurfer/subjects/fsaverage
 
 
then you don't have to worry about source and target. It will
implicitly create the symlink in $PWD
 
cheers
Bruce
On Fri, 19 Sep 2014, Mahmoud wrote:
 
  Bruce,
 
  By symlink from your /mnt/hgfs/mydata/fsaverage to
  /usr/local/freesurfer/subjects/fsaverage you mean
  ln -s
  /mnt/hgfs/mydata/fsaverageÂ
  /usr/local/freesurfer/subjects/fsaverage ?
  which fsaverage is the target ?
 
  Thanks,
  Mahmoud
 
  On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud
  zeydab...@gmail.com wrote:
  Â  Â  Â  Bruce,
  Thank you for your follow up and advice. Please let
  me know:
  1- How to download the fsaverage again?
  2- should I do the symlink manually or it will be
  done by recon-all
  later ?
  3- What steps should I take before running the
  recon-all -all ? should
  I create any specific directory? set any permission
  ?
 
  Best,
  Mahmoud
 
  On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl
  fis...@nmr.mgh.harvard.edu wrote:
  Â  Â  Â  yes, you symlinked it to itself which is why
  you are
  Â  Â  Â  getting the infinite recursion error. You
 need
  to delete
  Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage
 
  Â  Â  Â  and download the fsaverage dir again, put it
  in that
  Â  Â  Â  directory, then symlink from your
  Â  Â  Â  /mnt/hgfs/mydata/fsaverage to
  Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage
 
  Â  Â  Â  cheers
  Â  Â  Â  Bruce
  Â  Â  Â  On Fri, 19 Sep 2014, Mahmoud wrote:
 
  Â  Â  Â  Â  Â  Â  Bruce,
 
  Â  Â  Â  Â  Â  Â  I already had my data in a shared
 folder
  Â  Â  Â  Â  Â  Â  (/mnt/hgfs/mydata) but I got the
  Â  Â  Â  Â  Â  Â  permission error the same point
 that I
  got the
  Â  Â  Â  Â  Â  Â  symlink error lastly. So, I
  Â  Â  Â  Â  Â  Â  tought that might be due to
 something
  

Re: [Freesurfer] problems about freeview

[zkaufman]

Hello Rujing,

You can download the most up to date version of freeview using the
following link:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/dev/

In order to use this version, you will need to replace the file
$FREESURFER_HOME/bin/freeview.bin currently on your system, with the file
you download from the link above. Let me know if you need additional
assistance.


-Zeke



 Hi Rujing,

 I am able to replicate the issue with 5.3.0 release. The good news is the
 issue does not appear in the current dev version (so I think it has been
 fixed). Zeke, would it be possible for Rujing to download a copy of the
 latest freeview build?

 Best,
 Ruopeng

 On Jan 4, 2014, at 10:40 AM, charujing charuj...@gmail.com wrote:

 Dear doug, bruce and others,
 Previously I could not view 
 freeview -f
 $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
  from the
 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis;. The
 freeview did represent 3 images. But it reported a something about no
 geomatric information and I couldnot configure the overlay(When I
 clicked the configure overlay, it stopped without any response). My OS
 is CentOS 6.5 desktop version, and graphic card is NVIDIA GEFORCE GTX
 650 and setup the NVIDIA driver. Freesurfer version is
 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer has
 2G memory and 4 processors.
 I need help to fix it.
 If anyone have viewed sample data or other data(*.inflated,
 *sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by
 freeview just as above, would you please tell me some information? The
 information I need is Freesurer version, Centos version(desktop or
 others) and something in CentOS setup, graphic card version and its
 driver, memory size.
 Thanks very much, doug, brucen and others.
 Any reply will be highly appreciated.
 All the best.
 Rujing Zha
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Fw: Re: Re: problems about freeview

[zkaufman]

Rujing,

The freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz package
should be valid for all CentOS6.x versions, desktop and server editions. I
am not familiar with 'alternate' so I can not comment on that.

-Zeke






 发件人：charujingcharuj...@gmail.com
 发送时间：2014-01-05 09:55
 主题：Re: Re: [Freesurfer] problems about freeview
 收件人：zkaufmanzkauf...@nmr.mgh.harvard.edu,Ruopeng
 Wangrpw...@nmr.mgh.harvard.edu,charujingcharuj...@gmail.com
 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu

 Hi Ruopeng and Zeke,
 Thanks. I will try the latest version. CentOS has 6.0,6.1,6.2,6.3,6.4 and
 6.5, also part of them have desktop, server and alternate version. And in
 Freesurfer download page we can see:
 OSPlatformVersionRelease DateDownloadSize
 LinuxCentOS 6 x86_64 (64b)stable v5.3.015 May
 2013freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz4.2G
 LinuxCentOS 4 x86_64 (64b)stable v5.3.015 May
 2013freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz4.0G
 LinuxCentOS 4 (32b)stable v5.3.015 May
 2013freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz3.8G
 MacLion OX X 10.7 (64b Intel)stable v5.3.015 May
 2013freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg3.5G
 MacSnowLeopard OS X 10.6 (32b Intel)stable v5.3.015 May
 2013freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg3.2G
 VirtualboxXubuntu 12.04stable v5.3.015 Aug
 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G

 Also I want to know which CentOS version(6.0,6.1,6.2,6.3,6.4 or 6.5?) and
 its desktop, alternate or server I should installed or all of them are
 appropriate for freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.
 Thanks Ruopeng and Zeke.
 All the best.
 Rujing Zha

 2014-01-05



 charujing



 发件人：zkauf...@nmr.mgh.harvard.edu
 发送时间：2014-01-05 07:10
 主题：Re: [Freesurfer] problems about freeview
 收件人：charujingcharuj...@gmail.com
 抄送：Ruopeng
 Wangrpw...@nmr.mgh.harvard.edu,freesurferfreesurfer@nmr.mgh.harvard.edu,Z
 Kzkauf...@nmr.mgh.harvard.edu

 Hello Rujing,

 You can download the most up to date version of freeview using the
 following link:

 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/dev/

 In order to use this version, you will need to replace the file
 $FREESURFER_HOME/bin/freeview.bin currently on your system, with the file
 you download from the link above. Let me know if you need additional
 assistance.


 -Zeke



 Hi Rujing,

 I am able to replicate the issue with 5.3.0 release. The good news is
 the
 issue does not appear in the current dev version (so I think it has been
 fixed). Zeke, would it be possible for Rujing to download a copy of the
 latest freeview build?

 Best,
 Ruopeng

 On Jan 4, 2014, at 10:40 AM, charujing charuj...@gmail.com wrote:

 Dear doug, bruce and others,
 Previously I could not view 
 freeview -f
 $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
  from the
 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis;.
 The
 freeview did represent 3 images. But it reported a something about no
 geomatric information and I couldnot configure the overlay(When I
 clicked the configure overlay, it stopped without any response). My
 OS
 is CentOS 6.5 desktop version, and graphic card is NVIDIA GEFORCE GTX
 650 and setup the NVIDIA driver. Freesurfer version is
 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer
 has
 2G memory and 4 processors.
 I need help to fix it.
 If anyone have viewed sample data or other data(*.inflated,
 *sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by
 freeview just as above, would you please tell me some information? The
 information I need is Freesurer version, Centos version(desktop or
 others) and something in CentOS setup, graphic card version and its
 driver, memory size.
 Thanks very much, doug, brucen and others.
 Any reply will be highly appreciated.
 All the best.
 Rujing Zha
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer





 The 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 Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
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Re: [Freesurfer] tksurfer and mountain lion problem / question

[zkaufman]

Hello Sal,

I tried setting my display to :0.0 and was able to get the tkmedit program
to open on my Mac Mountain Lion machine so Im not exactly sure why yours
is having difficulty. Have you installed XQuartz?

http://xquartz.macosforge.org/landing/

If you already have XQuartz installed I would go ahead and try commenting
out the DISPLAY variable setting in the /etc/profile file and reopen a
terminal and see if that works.

-Zeke



 Hi,

 I can run freeview using my current install on Mountain Lion, however when
 I run tkmedit or tksurfer I get the following error:

 GLUT: Fatal Error in tksurfer.bin: could not open display: :0.0

 my /etc/profile has the setting export DISPLAY=:0.0  for a different
 program. Is there settings I should add / change to allow tkmedit or
 tksurfer to run?

 Thanks!

 Sal
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Re: [Freesurfer] Qdec error

[zkaufman]

Hello,

Is this running in Ubuntu? If so, it should be solved by running the
following command:

$ sudo apt-get install libjpeg62

-Zeke

 Dear All,

 When I tried to running qdec, I'm getting the following error.

 qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
 shared object file: No such file or directory


 What is the solution for this.?

 Any help will be greatly appreciated.
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Installation trouble on Macbook Air (no such file or directory)

[zkaufman]

Nate,

Try typing the following from the command window:

export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Or, you can add these lines to your .bashrc file in your home directory by
using any text editor, or by typing the following in the command line:

echo export FREESURFER_HOME=/Applications/freesurfer  ~/.bashrc
echo source $FREESURFER_HOME/SetUpFreeSurfer.sh  ~/.bashrc

Once these lines are in your .bashrc file, freesurfer will load everytime
you open the terminal program.

-Zeke





 I am new to Unix and FreeSurfer, and I am having some trouble installing
 FreeSurfer on my Macbook Air (10.8). I've downloaded the .dmg file just
 fine, and when I start the installation steps, I'm instructed to add some
 lines to my .cshrc or .tcshrc files in my home directory. Can anyone point
 me to this file? Also, just below on the installation dialog, it says for
 sh or bash users:

 export FREESURFER_HOME=freesurfer_installation_directory/freesurfer
 source $FREESURFER_HOME/SetUpFreeSurfer.sh


 Can I use these instead of the first two lines of code? I tried to enter
 these bash lines one at a time into my terminal window. The first one
 (export) did not give me any errors but for the source one, I received
 the message:

 bash: /freesurfer/SetUpFreeSurfer.sh: No such file or directory.

 Any idea as to why I am getting this error? My apologies in advance for my
 lack of experience.

 Many thanks,
 Nate
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Re: [Freesurfer] Download difficulty

[zkaufman]

Mike,

I have tested the download from multiple computers on multiple different
networks, including my home network. It is successful everytime. I dont
know if you have a a system administrator who can help resolve the
situation on your end but everything seems to be running correctly on our
side.

-Zeke


 Hello all, I seem to be having some difficulty downloading the freesurfer
 software to my MAC computers.  I have tried my laptop (MacBook pro, I
 don't
 remember the version but it is approx. 10.3) as well as a desktop (imac,
 mac osx version 10.8.3) and also tried two different networks.  I have
 tried just clicking on the link (on your download page) as well as the
 curl
 -O command line.  I get an NSURL error everytime, prior to any significant
 downloading.  I have not have this difficulty with other freeware
 downloading to the same computers or on these networks.  Any thoughts?

 Thanks
 Mike
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[Freesurfer] Fwd: Re: mris_resample: Command not found.

[zkaufman]

Daniel, Stefano, Others,

A patch is now available for the mris_resample : Command not found 
error you encountered.

Simply download the file from the following link and place it in your
$FREESURFER_HOME/bin directory:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample

Feel free to contact me if you have any additional questions/issues.

-Zeke


 Original Message 
Subject: Re: [Freesurfer] mris_resample: Command not found.
Date: Tue, 28 May 2013 11:41:21 -0400
From: Z K zkauf...@nmr.mgh.harvard.edu
To: Barron, Daniel S barr...@livemail.uthscsa.edu
CC: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu,
 Lilla Zollei lzol...@nmr.mgh.harvard.edu

Hello Daniel,

This is a confirmed issue with the 64bit Mac build. A patch to fix the
issue will be available shortly (~hours). I will email the list and you
personally once it is available. Sorry for the inconvenience.

-Zeke

On 05/28/2013 11:36 AM, Barron, Daniel S wrote:
 Hi Lilla,
 I'm using OSX 10.8.3
 Thanks,
 Daniel
 
 From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu]
 Sent: Tuesday, May 28, 2013 10:04 AM
 To: Barron, Daniel S
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: mris_resample: Command not found.
 Hi Daniel,
 What operating system are you using?
 Lilla
 On Tue, 28 May 2013, Barron, Daniel S wrote:
 Hello,
 I am trying to perform an inter-subject registration using
mri_cvs_register on version 5.3.
 When I ran mri_cvs_check, my feedback was I needed to find
mri_cvs_register.settings.txt but I didn't worry about this per
Lilla's post:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html
 mri_cvs_register kicks off well, but eventually it ends with:
 mris_resample: Command not found.
 I go into my $FREESURFER_HOME/bin directory and note that mris_resample
is truly not there.  Did I not install 5.3 properly?
 I have attached a log file in case this helps.
 Cheers,
 Daniel
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Re: [Freesurfer] Freesurfer MAC installation

[zkaufman]

Flavia,

You are going to have to be a little more specific in describing what you
are trying to do and what exactly the problem is. You say you cannot open
the example Bert... What does that mean? You can open it in tkmedit? What
is the error?

The procedure for getting the license is to go to this page
(http://surfer.nmr.mgh.harvard.edu/registration.html). Fill out the form.
Get the email. Copy the license content from the email into a file called
.license (dont use the quotes). Place the .license fill in the
/Application/freesurfer directory.

It is a fairly simple process. If you
do not have a .license file in /Application/freesurfer directory, nothing
will work. So you must accomplish this first.

-Zeke

 Hi Zeke,

 many thanks for your answer
 but I still cannot use freesurfer, I cannot open the example Bert.
 I am not sure that the license is placed because I cannot open this. Could
 you please help me?
 how can I do?
 Which is theprocedure to put the license?
 Why I cannot open this file?
 HELP!

 On Fri, May 17, 2013 at 6:27 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:

 Hello Flavia,

 The .license file should be placed in the /Applications/freesurfer
 directory.

 To load freesurfer, you must open the terminal type the following :

   setenv FREESURFER_HOME /Applications/freesurfer
   source $FREESURFER_HOME/SetUpFreeSurfer.sh

 -Zeke


 On 05/17/2013 12:49 PM, Flavia Niccolini wrote:
  Hi
  I am having trouble with the license file.
  I created in Freesurfer a file named .license but I cannot open this
  and copy the license.
  where and how should I put the 3 lines license?
  I tried to test my freesurfer installation with Bert but I got as
 answer
  command non found.
  Please help
  BW
  Flavia
 
 
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Re: [Freesurfer] FS 5.2 tkmedit X11 - Xquartz Snow-Leopard

[zkaufman]

Gari,

This is definitely an XQuartz issue. Have you rebooted your system since
installing XQuartz? Does /opt/X11/lib/libGLU.1.dylib exist? In my
experience, installing XQuartz can be a finicky process that sometimes
requires at least one reboot and a logout/login. If rebooting doesn't
solve your issue I would completely uninstall XQuartz:

sudo rm -rf /System/Library/Launch*/org.x.*
sudo rm -rf /Applications/Utilities/XQuartz.app
sudo rm -rf /opt/X11
sudo rm /usr/X11
sudo rm /usr/X11R6

and reinstall XQuartz, and reboot! I wrote a short wiki page that
troubleshoots various freesurfer GUI issues on Mac Snow Leopard:

http://surfer.nmr.mgh.harvard.edu/fswiki/qdec_snowleopard

-Zeke



 Update: tkmedit 5.1 is working with Xquartz installed in Snow Leopard,
 tkmedit 5.2 is not working again.

 Any suggestion?

 thanks,
 Gari


 On Tue, Mar 12, 2013 at 1:16 PM, Garikoitz Lerma-Usabiaga 
 gariko...@gmail.com wrote:

 Hi FS experts,
 I just installed 5.2 for Snow Leopard in a machine who already had 5.1.

 When running tkmedit in 5.1 X11 works well, but when running it from 5.2
 it gives the following error:

 BRODMANN80:~ glerma$ tkmedit bert T1.mgz
 dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib
   Referenced from: /Users/glerma/Apps/freesurfer/tktools/tkmedit.bin
   Reason: image not found
 Trace/BPT trap


 I've seen in  the mail list that when this happens, Xquartz should be
 installed.

 But, is it a requirement for freesurfer 5.2 in Snow Leopard to run with
 Xquartz? Should I remove X11 and install Xquartz then? (it may affect
 other
 programs and I am reluctant to do it...)

 Many thanks,
 Gari

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Re: [Freesurfer] FS workshop registration link

[zkaufman]

Hello Nooshin,

The email containing the registration page went out today at 11am EST. It
can be found here:

https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.7678.cgi

Unfortunately, the course was filled within the first two hours of opening
registration, but there is a waitlist and you are free to sign up for
that.

I see your name and email in our email list so you should have received
today's announcement. Maybe check your spam folder?

-Zeke


 Dear All

 I have a question about upcoming Freesurfer course registration (April 29
 _
 May 1). The registration link was supposed to be open and sent by today,
 but I still have not received it.
 I was wondering if you have any information and can help me.

 Thanks a lot
 Nooshin
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Re: [Freesurfer] tkregister2 window error: Remote login

[zkaufman]

Hello Sudhin,

From what I can tell, it appears that is it possible you have a
compatibility issue between Exceed OpenGL and Mesa GLX (and thus not
directly a freesurfer issue).

It turns out if your system's libGL.so library is provided by Mesa
7.1 or later, OpenGL applications will not run remotely. Can you try to
run 'glxinfo' at the command line...? Do you get an error? If so try
setting the environment variable:

(example using bash)
export LIBGL_ALWAYS_INDIRECT=y

And then try running tkregister again. Hopefully this works

-Zeke


 Hello,

 I am remotely logged in to my Ubuntu system(from Mac). I have previously
 run tkregister2 but am now having trouble;

 Opening window subj
 Window type not found
 register: tkoinitwindow(name) failed.

 Is there a solution to this?

 Thanks,

 S
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[Freesurfer] [Fwd: Re: tkregister2 window error: Remote login]

[zkaufman]

cc'ing the freesurfer list so other with the same issue may reference.

 Original Message 
Subject: Re: [Freesurfer] tkregister2 window error: Remote login
From:Sudhin A. Shah sut2...@med.cornell.edu
Date:Fri, February 22, 2013 10:51 am
To:  zkauf...@nmr.mgh.harvard.edu zkauf...@nmr.mgh.harvard.edu
--

Thank you!! This worked :)


On Feb 22, 2013, at 10:14 AM, zkauf...@nmr.mgh.harvard.edu
zkauf...@nmr.mgh.harvard.edu wrote:

 Hello Sudhin,

 From what I can tell, it appears that is it possible you have a
 compatibility issue between Exceed OpenGL and Mesa GLX (and thus not
 directly a freesurfer issue).

 It turns out if your system's libGL.so library is provided by Mesa
 7.1 or later, OpenGL applications will not run remotely. Can you try to
 run 'glxinfo' at the command line...? Do you get an error? If so try
 setting the environment variable:

 (example using bash)
 export LIBGL_ALWAYS_INDIRECT=y

 And then try running tkregister again. Hopefully this works

 -Zeke


 Hello,

 I am remotely logged in to my Ubuntu system(from Mac). I have previously
 run tkregister2 but am now having trouble;

 Opening window subj
 Window type not found
 register: tkoinitwindow(name) failed.

 Is there a solution to this?

 Thanks,

 S
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Re: [Freesurfer] GLUT: Fatal error in tkmedit.bin: visual with necessary capabilities not found

[zkaufman]

Hello Kalli,

In the past this issue has been related to out-of-date NVIDIA drivers. If
you open a terminal and type 'glxgears' do you see a window pop-up
with 3 colored gears running? If not, email the help desk and ask them to
update your NVIDIA drivers.

-Zeke


 Hi all,
 I am a new student at the Martinos and very new to the freesurfer
 community - I am actually in the learning process for the moment.
 Today after passing the tkmedit command I keep getting the following
 message:
 GLUT: Fatal error in tkmedit.bin: visual with necessary capabilities not
 found.
 This is bizarre since I have been perfectly able to use tkmedit and
 tksurfer previously.
 I am using CentOS 6.3.
 Any suggestions are more than welcome!
 Kalli
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Re: [Freesurfer] Download v. 5.0 on Mac Lion 10.7.5

[zkaufman]

Hello Krista,

freesurfer v5.0 does not have a Lion build. Im fairly certain Lion did not
even exist when 5.0 was released. I suggest you give the Leopard build a
try, I *think* it will work, but I haven't tested it.

If you download the the .dmg file the install should be fairly self
explanatory. A couple clicks of I agree and Continue and you should be
all set.

-Zeke

 Hello,

 I need to download an older version of freesurfer (Version 5.0) on a Mac
 Lion 10.7.5. In the archives I don't see a file for Lion, just Leopard and
 Tiger. Is it possible that either of these will work for Lion? Also, are
 there any step by step instructions on how to install?

 Thanks!
 Krista
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Re: [Freesurfer] Download v. 5.0 on Mac Lion 10.7.5

[zkaufman]

I just noticed their are two Leopards builds... go with the leopard-i686
version.

-Zeke


 Hello Krista,

 freesurfer v5.0 does not have a Lion build. Im fairly certain Lion did not
 even exist when 5.0 was released. I suggest you give the Leopard build a
 try, I *think* it will work, but I haven't tested it.

 If you download the the .dmg file the install should be fairly self
 explanatory. A couple clicks of I agree and Continue and you should be
 all set.

 -Zeke

 Hello,

 I need to download an older version of freesurfer (Version 5.0) on a Mac
 Lion 10.7.5. In the archives I don't see a file for Lion, just Leopard
 and
 Tiger. Is it possible that either of these will work for Lion? Also, are
 there any step by step instructions on how to install?

 Thanks!
 Krista
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Re: [Freesurfer] problem with qdec in full install of 5.2 beta

[zkaufman]

Hello Carl,

Some of the freesurfer GUIs require XQuartz. Unfortunately, XQuartz is no
longer installed by default on Mac 10.8. You can download and install
XQuartz from here:

http://xquartz.macosforge.org/landing/

-Zeke



 Dear Freesurfer,

 When trying to start qdec I get the following error:

 dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib
   Referenced from: /Applications/freesurfer/bin/qdec.bin
   Reason: image not found
 Trace/BPT trap

 Any suggestions for a work around?

 Thanks,

 Carl

 --
 •~~•~~•~~•~~•~~•~~•~~•
 Carl M. Anderson, Ph.D. (mail stop 204)
 Assistant Professor of Psychiatry,
 Harvard Medical School 
 The Neuroimaging Center,
 McLean Hospital 115 Mill St.  Belmont, MA 02478
 Ph: 617-855-2972;  Fax: 617-855-2770
 e-mail: remfr...@gmail.com; carl_ander...@hms.harvard.edu
 •~~•~~•~~•~~•~~•~~•~~•
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