[Freesurfer] Recall: freeview upgrade isn’t working/library issue

[Hoptman, Matthew (NKI)]

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Hoptman, Matthew (NKI) would like to recall the message, "freeview upgrade 
isn’t working/library issue".



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[Freesurfer] freeview upgrade isn’t working/library issue

[Hoptman, Matthew (NKI)]

External Email - Use Caution

TO: freesurfer@nmr.mgh.harvard.edu
FROM: matthew.hopt...@nki.rfmh.org
SUBJECT: freeview upgrade isn’t working/library issue

Hello FreeSurfer Developers,

I followed the instructions here to upgrade freeview:
https://secure-web.cisco.com/1Fr1m43dMDo6PfZjwvbGiKtV6gtUUqAq08NIpRJf8nkhbpl6t_xCxggb1kwbhGAFGwTRhGkv4sWJDCjuHWTgohXGwrq-nAIvtq0Nfdd0_tSvmjvKWkv0IlMgpiIVnUf21uW4udZFN11ePTzTN75eirFuiyPk5w32ox5i_idq8DjZL2rE1Lhw9aSRLi3dL4VfG-EQQoTkGSI8C9oJRQKc6GjfomWHQ9wZBHqlQ-up71hJye297HHynBTUWYmHHjdXxRE8hiF6oPiasyVgS3wzts8TCnn2zZEmlDUcp4aN9Vjx2Xj6vUXf5no1SeK6B6hk0/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUpdateFreeview

I am now getting the error:
freeview: error while loading shared libraries: 
libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file 
or directory

I saw that it was recommended to install the package libvtk7.1, but that isn’t 
working:
E: Unable to locate package libvtk7.1
E: Couldn't find any package by glob 'libvtk7.1'

Any help is appreciated. I am using:
5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 
x86_64 GNU/Linux

Thanks,
Matt


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[Freesurfer] Freesurfer 6.0

[Hoptman, Matthew]

Hi all,
I can see a link for Freesurfer 6.0 on the website, but when I click on it to 
download, it just blinks at me.  I also tried to ftp to your ftp site, and 
unfortunately, I got the message
421 Proxy is closed (unknown user location).

Could you please tell me how I could get the new version of Freesurfer?
Thanks,
Matt
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Re: [Freesurfer] application of mri_cvs_register question

[Hoptman, Matthew]

Thanks, Anastasia,
That worked.  Sorry I missed it!!
--Mat

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 3:17 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] application of mri_cvs_register question


Hi Matt - Try anatorig2diff.bbr.dat.

a.y

On Mon, 15 Jul 2013, Hoptman, Matthew wrote:

> Hi Anastasia,
> Here it is:
> anat2anatorig.dat   anatorig2diff.bbr.dat  anatorig2diff.bbr.dat.sum  
> diff2mni.bbr.mat
> anat2anatorig.dat~  anatorig2diff.bbr.dat~ anatorig2diff.bbr.mat  
> mni2anat.mat
> anat2anatorig.mat   anatorig2diff.bbr.dat.log  anatorig2mni.mat   
> mni2anatorig.mat
> anat2diff.bbr.mat   anatorig2diff.bbr.dat.log.old  cvs
> mni2diff.bbr.mat
> anat2mni.matanatorig2diff.bbr.dat.mincost  diff2anat.bbr.mat
> anatorig2anat.mat   anatorig2diff.bbr.dat.paramdiff2anatorig.bbr.mat
>
> -Original Message-
> From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, July 15, 2013 2:56 PM
> To: Hoptman, Matthew
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] application of mri_cvs_register question
>
>
> Got it. Can you send me a listing of the contents of the xfms/ directory?
> Conversions b/w formats can be done with tkregister2, but the .dat file
> should normally be there since it's the default format for bbregister.
>
> On Mon, 15 Jul 2013, Hoptman, Matthew wrote:
>
>> Right, that's been my problem :(  Maybe something went wrong, but I didn't 
>> see any problem in the log files.  Actually, the command I showed below had 
>> a typo (I used --mat rather than --reg to get that error).  Is there a way 
>> to  convert *.mat to *.dat?
>>
>> -Original Message-
>> From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
>> Sent: Monday, July 15, 2013 2:44 PM
>> To: Hoptman, Matthew
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: RE: [Freesurfer] application of mri_cvs_register question
>>
>>
>> Hi Matt - The --reg option expects a .dat file. There should be one
>> produced by bbregister in the xfms/ directory?
>>
>> a.y
>>
>> On Mon, 15 Jul 2013, Hoptman, Matthew wrote:
>>
>>> Hi Anastasia,
>>> Yes, that was my problem. I think I need to use
>>> mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z
>>> ../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z
>>> --noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o
>>> diffvol2CVS.nii.gz --no-save-reg
>>>
>>>
>>> I now get:
>>> Using the m3z file as it is; no assumed location.
>>> regio_read_register(): Success
>>> Error reading R[3][0] from diff2anat.bbr.mat
>>>
>>> Matrix from regfile:
>>> -0.001   0.972  -0.234  -3.311;
>>> -0.001   0.234   0.972   69.949;
>>> 0.000   0.000   0.000   1.000;
>>> 0.000   0.000   0.000   0.000;
>>>
>>> I was stuck at that point.  Lilla Zollei told me she'd look into it, but 
>>> maybe you've communicated with her?
>>> Thanks
>>> Matt
>>>
>>> -Original Message-
>>> From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
>>> Sent: Monday, July 15, 2013 2:30 PM
>>> To: Hoptman, Matthew
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: RE: [Freesurfer] application of mri_cvs_register question
>>>
>>>
>>> Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to
>>> the CVS template. To map from individual diffusion to the CVS template,
>>> you'd have to first use diffusion-to-anatomical affine transform file
>>> under xfms/.
>>>
>>> Hope this helps,
>>> a.y
>>>
>>> On Mon, 15 Jul 2013, Hoptman, Matthew wrote:
>>>
>>>> Hi Anastasia,
>>>> Not really, what I now have is:
>>>> /dmri/xfms/cvs
>>>> Within cvs, there are anatomical files that are registered to the CVS 
>>>> template, as below, but what I DON'T have is the application of these 
>>>> transforms to the DTI data.  That's what I'm trying to puzzle out.
>>>>
>>>> The files in /dmri/xfms/cvs are:
>>>> c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log
>>>> c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
>>>> final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz
>>>> final_CVSmorphed_tocvs_avg35_in

Re: [Freesurfer] application of mri_cvs_register question

[Hoptman, Matthew]

Hi Anastasia,
Yes, that was my problem. I think I need to use
mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z
 ../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z
--noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o
 diffvol2CVS.nii.gz --no-save-reg


I now get:
Using the m3z file as it is; no assumed location.
regio_read_register(): Success
Error reading R[3][0] from diff2anat.bbr.mat

Matrix from regfile:
-0.001   0.972  -0.234  -3.311;
-0.001   0.234   0.972   69.949;
 0.000   0.000   0.000   1.000;
 0.000   0.000   0.000   0.000;

I was stuck at that point.  Lilla Zollei told me she'd look into it, but maybe 
you've communicated with her?
Thanks
Matt

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 2:30 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] application of mri_cvs_register question


Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to
the CVS template. To map from individual diffusion to the CVS template,
you'd have to first use diffusion-to-anatomical affine transform file
under xfms/.

Hope this helps,
a.y

On Mon, 15 Jul 2013, Hoptman, Matthew wrote:

> Hi Anastasia,
> Not really, what I now have is:
> /dmri/xfms/cvs
> Within cvs, there are anatomical files that are registered to the CVS 
> template, as below, but what I DON'T have is the application of these 
> transforms to the DTI data.  That's what I'm trying to puzzle out.
>
> The files in /dmri/xfms/cvs are:
> c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log
> c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
> final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz
> final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz
> final_CVSmorph_tocvs_avg35_inMNI152.m3z
> lh.dbg_surf.pial
> lh.dbg_surf.white
> lh.resample.aparc.annot
> lh.resample.pial
> lh.resample.white
> nlalign-afteraseg-norm.mgz
> nlalign-aseg.mgz
> rh.dbg_surf.pial
> rh.dbg_surf.white
> rh.resample.aparc.annot
> rh.resample.pial
> rh.resample.white
> summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log
> summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
> transform.txt
>
>
> -Original Message-
> From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, July 15, 2013 12:19 PM
> To: Hoptman, Matthew
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] application of mri_cvs_register question
>
>
> Hi Matt - For how to tell tracula to use CVS registration, see "Specify
> the inter-subject registration method" here:
>http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
>
> Does this answer your question?
>
> a.y
>
> On Mon, 8 Jul 2013, Hoptman, Matthew wrote:
>
>>
>> Hi all,
>>
>> I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear 
>> on how to do so to DTI data processed in Tracula.  The command in the 
>> “Multimodal
>> integration and inter-subject registration” tutorial is:
>>
>> mri_vol2vol   --targ templateid --m3z morph.m3z --noDefM3zPath --reg 
>> 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg
>>
>>
>>
>> But in Tracula, there are no “register.dat” files, or indeed no *.dat files. 
>>  Is there a way to convert one of the *.mat files in the dmri/xfms directory 
>> to a
>> *.dat file?  Also, given that I think Tracula and dt_recon use different 
>> transformation algorithms, which Tracula transform should I choose?
>>
>>
>>
>> Thanks,
>>
>> Matt
>>
>>
>>
>> Matthew J. Hoptman, PhD
>> Research Scientist V
>> Nathan S. Kline Institute for Psychiatric Research
>>
>> Research Associate Professor in Psychiatry
>> NYU School of Medicine
>>
>>
>>
>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
>> recipient. It may contain confidential information which is legally 
>> privileged or
>> otherwise protected by law. If you received this
>> e-mail in error or from someone who was not authorized to send it to you, 
>> you are strictly prohibited from reviewing, using, disseminating, 
>> distributing or
>> copying the e-mail.
>>
>> PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
>> MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
>>
>>
>>
>> _
>> Cons

Re: [Freesurfer] application of mri_cvs_register question

[Hoptman, Matthew]

Hi Lilla,
Unfortunately, when I run:
mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z 
../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z 
--noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o 
diffvol2CVS.nii.gz --no-save-reg

I now get:
Using the m3z file as it is; no assumed location.
regio_read_register(): Success
Error reading R[3][0] from diff2anat.bbr.mat

Matrix from regfile:
-0.001   0.972  -0.234  -3.311;
-0.001   0.234   0.972   69.949;
 0.000   0.000   0.000   1.000;
 0.000   0.000   0.000   0.000;

Best,
Matt
-Original Message-
From: Lilla Zollei [mailto:lzol...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 10, 2013 6:07 PM
To: Hoptman, Matthew
Subject: RE: [Freesurfer] application of mri_cvs_register question


Hi Matt,

As diff2anat.bbr.mat was created by bbregister, I believe you should be
able to use --reg diff2anat.bbr.mat in your command.

Let me know if you encounter further problems.

Lilla

On Wed, 10 Jul 2013, Hoptman, Matthew wrote:

> Hi Lilla,
> I want to apply the transform to both the dtifit_FA and tracula tracts to put 
> them into cvs space (given the m3z file, as well).  The goal is to get 
> "average" tracts across my subjects.  The relevant transforms I have in my 
> dmri/xfms would  seem to be:
> diff2anat.bbr.mat
> diff2anatorig.bbr.mat
> diff2mni.bbr.mat
>
> Thanks,
> Matt
> -Original Message-
> From: Lilla Zollei [mailto:lzol...@nmr.mgh.harvard.edu]
> Sent: Tuesday, July 09, 2013 8:01 PM
> To: Hoptman, Matthew
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] application of mri_cvs_register question
>
>
> Hi,
>
> What type of registration file do you have representing the diff2anat
> transformation? With mri_vol2vol you can use many different types of
> transformations, if you switch the --reg flag to --xfm, --fsl or --lta,
> for example.
>
> Lilla
>
> On Mon, 8 Jul 2013, Hoptman, Matthew wrote:
>
>>
>> Hi all,
>>
>> I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear 
>> on how to do so to DTI data processed in Tracula.  The command in the 
>> “Multimodal integration and inter-subject registration” tutorial is:
>>
>> mri_vol2vol   --targ templateid --m3z morph.m3z --noDefM3zPath --reg 
>> 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg
>>
>>
>>
>> But in Tracula, there are no “register.dat” files, or indeed no *.dat files. 
>>  Is there a way to convert one of the *.mat files in the dmri/xfms directory 
>> to a *.dat file?  Also, given that I think Tracula and dt_recon use 
>> different transformation algorithms, which Tracula
>> transform should I choose?
>>
>>
>>
>> Thanks,
>>
>> Matt
>>
>>
>>
>> Matthew J. Hoptman, PhD
>> Research Scientist V
>> Nathan S. Kline Institute for Psychiatric Research
>>
>> Research Associate Professor in Psychiatry
>> NYU School of Medicine
>>
>>
>>
>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
>> recipient. It may contain confidential information which is legally 
>> privileged or otherwise protected by law. If you received this
>> e-mail in error or from someone who was not authorized to send it to you, 
>> you are strictly prohibited from reviewing, using, disseminating, 
>> distributing or copying the e-mail.
>>
>> PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
>> MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
>>
>>
>>
>> __
>> Conserve Resources. Print only when necessary.
>>
>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
>> recipient. It may contain confidential information which is legally 
>> privilegedor otherwise protected by law. If you received this e-mail in 
>> error or from someone who is not authorized to send it to you, you
>> are strictly prohibited from reviewing, using, disseminating, distributing 
>> or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN 
>> E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your 
>> cooperation.
>>
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>> recipient. It may contain confidential information which is legally 
>> privileged or otherwise protected by law. If you receiv

[Freesurfer] application of mri_cvs_register question

[Hoptman, Matthew]

Hi all,
I see how to apply mri_vol2vol to DTI data from dt_recon, but I'm not clear on 
how to do so to DTI data processed in Tracula.  The command in the "Multimodal 
integration and inter-subject registration" tutorial is:
mri_vol2vol   --targ templateid --m3z morph.m3z --noDefM3zPath --reg 
2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg

But in Tracula, there are no "register.dat" files, or indeed no *.dat files.  
Is there a way to convert one of the *.mat files in the dmri/xfms directory to 
a *.dat file?  Also, given that I think Tracula and dt_recon use different 
transformation algorithms, which Tracula transform should I choose?

Thanks,
Matt

Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
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are strictly prohibited from reviewing, using, disseminating, distributing or 
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Conserve Resources. Print only when necessary.

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[Freesurfer] libboost_programs_options.so.5 problem solved, at least for me

[Hoptman, Matthew]

Hi,
I never got an answer to this problem, which affected numerous programs 
including mris_resample, but I solved it with help from my local sysadmin.

I think the problem is that there is a versioning difference between Centos and 
other Linux "flavors" (I use Linux Mint 14).  But anyway, I:

1)   got the following RPM:
boost-program-options-1.41.0-17.el6_4.x86_64.rpm

2)  Extracted the relevant file:

sudo rpm2cpio boost-program-options-1.41.0-17.el6_4.x86_64.rpm | cpio -ivd 
/usr/lib/libboost_program_options.so.5

3)  Verified the file (libboost_program_options.so.5) was in /usr/lib


And then I was good to go.  Hope this helps others.
--Matt


Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
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Conserve Resources. Print only when necessary.

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Re: [Freesurfer] libboost_program_options.so.5 issue

[Hoptman, Matthew]

Hi all,
Any update on this issue?  At present, I'm not able to use mri_cvs_register as 
a result of the problem (several other programs also require this library).
Best,
Matt

From: Hoptman, Matthew
Sent: Tuesday, June 18, 2013 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: libboost_program_options.so.5 issue

Hi all,
Any news on the libboost_program_options.so.5 issue, as relates to 
mri_cvs_register?  I've encountered it using mris_resample (as part of 
mri_cvs_register) using.
When I run:
qsub -S /bin/tcsh -pe make 2 -b y -v PATH=${FREESURFER_HOME}/bin:$PATH -V 
${FREESURFER_HOME}/bin/mri_cvs_register --mov ${subject}

where ${subject} was found by looping through all of my subjects

I get the error:
mris_resample: error while loading shared libraries: 
libboost_program_options.so.5: cannot open shared object file: No such file or 
directory

bugr gives me:

FREESURFER_HOME: /home/hoptman/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0beta
Debian version: 6.0.4
Kernel info: Linux 2.6.32-5-amd64 x86_64

Thanks,
Matt
Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine

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[Freesurfer] libboost_program_options.so.5 issue

[Hoptman, Matthew]

Hi all,
Any news on the libboost_program_options.so.5 issue, as relates to 
mri_cvs_register?  I've encountered it using mris_resample (as part of 
mri_cvs_register) using.
When I run:
qsub -S /bin/tcsh -pe make 2 -b y -v PATH=${FREESURFER_HOME}/bin:$PATH -V 
${FREESURFER_HOME}/bin/mri_cvs_register --mov ${subject}

where ${subject} was found by looping through all of my subjects

I get the error:
mris_resample: error while loading shared libraries: 
libboost_program_options.so.5: cannot open shared object file: No such file or 
directory

bugr gives me:

FREESURFER_HOME: /home/hoptman/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0beta
Debian version: 6.0.4
Kernel info: Linux 2.6.32-5-amd64 x86_64

Thanks,
Matt
Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine

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[Freesurfer] averaging tracts?

[Hoptman, Matthew]

Hi all,
Thanks for tracula , which I think is a terrific tool.  Is there any way to 
average tracts across subjects for viewing purposes?  I have in mind somehting 
along the line of a group average merged_avg33_mni_bbi.mgz.
Thanks,
Matt

Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine

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Re: [Freesurfer] Tracula problem

[Hoptman, Matthew]

Gotcha, Thanks.

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, May 20, 2013 10:06 AM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula problem


Hi Matt - Yes, the dcmroot variable can be used if you have the same root
directory for *all* input files. If not, don't define dcmroot and instead
give the full path to each input file. Then you shouldn't have to modify
any scrips.

a.y

On Fri, 17 May 2013, Hoptman, Matthew wrote:

> Hi Anastasia,
> I solved this particular problem in a new dmrirc, but it seemed that I had to 
> modify trac-all to remove the ${dcmroot} in front of:
> infile, b0mfile and b0pfile:
>
> diff bin/trac-preproc bin/trac-preproc.orig
>
> <   if ($#dcmroot > 0) set infile = $infile
> ---
>>   if ($#dcmroot > 0) set infile = $dcmroot/$infile
> 259c259
> <endif
> ---
>> endif
> 296c296
> < set dcmfile = $b0mfile
> ---
>> set dcmfile = $dcmroot/$b0mfile
> 311c311
> < set dcmfile = $b0pfile
> ---
>> set dcmfile = $dcmroot/$b0pfile
>
> But now it doesn't seem to loop through the subjects, so I'm doing them one 
> at a time (painful).
>
> Also, if, as in my other question, I try to run this as a cluster job, I 
> don't know how I can substitute a new subject into  subjlist.  I have 64 
> subjects and would like to do trac-all -prep -c dmri on all of them 
> simultaneously.  I have used bedpostx in SGE, but there you can just write 
> loop to get it to go through your subjects.
>
> If I could make the subject variable external to dmrirc, I could do easily 
> script the trac-all job to run in SGE, but I can't fiugre out how to pass it 
> to the trac-all command.  Is there any way to pass the subject number 
> directly to the command?
> Does this make sense?
> Matt
>
> -Original Message-
> From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
> Sent: Friday, May 17, 2013 12:31 PM
> To: Hoptman, Matthew
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Tracula problem
>
>
> Hi Matt - Can you source try this on the command line:
>source dmrirc_53beta
>echo $b0mlist
>echo $b0plist
>
> Are these filenames correct, do these files exist? This is how you define
> them in your configuration file:
> set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`)
> set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`)
>
> Thanks,
> a.y
>
> On Wed, 15 May 2013, Hoptman, Matthew wrote:
>
>>
>> Hi all,
>>
>>
>>
>> I’m having a problem with tracula.  I’m trying to run in version 5.3 beta 
>> (is that
>> version very different from the newer 5.3?).  If I run
>>
>> trac-preproc   -c dmrirc –prep,
>>
>>
>> I get:
>>
>> mri_convert /home/hoptman/freesurfer/subjects/c159032/
>> /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
>>
>> mri_convert /home/hoptman/freesurfer/subjects/c159032/
>> /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
>>
>> corRead(): can't open file 
>> /home/hoptman/freesurfer/subjects/c159032/COR-.info
>>
>>
>>
>> I don’t know why it would look for COR-.info in the subjects’ root 
>> directory.  I’m
>> attaching my dmrirc file in case that helps.
>>
>>
>>
>> Thanks,
>> Matt
>>
>> Matthew J. Hoptman, PhD
>> Research Scientist V
>> Nathan S. Kline Institute for Psychiatric Research
>>
>> Research Associate Professor in Psychiatry
>> NYU School of Medicine
>>
>>
>>
>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
>> recipient.
>> It may contain confidential information which is legally privileged or 
>> otherwise
>> protected by law. If you received this
>> e-mail in error or from someone who was not authorized to send it to you, 
>> you are
>> strictly prohibited from reviewing, using, disseminating, distributing or 
>> copying
>> the e-mail.
>>
>> PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
>> MESSAGE
>> FROM YOUR SYSTEM. Thank you for your cooperation.
>>
>>
>>
>> __
>> Conserve Resources. Print only when necessary.
>>
>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
>> recipient.
>> It may contain confidential information which is legally privilegedor 
>> otherwise
>>

Re: [Freesurfer] any way to parallelize Tracula?

[Hoptman, Matthew]

Hi all,
Good news.  I was able to submit the job to our cluster using the -s flag of 
the trac-all command.  Once I did that, I just wrote a loop to go through my 
subjects and was good to go.
--Matt

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 1:02 PM
To: Susan Kuo
Cc: Hoptman, Matthew; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] any way to parallelize Tracula?


Hi Susie - The underlying script doing the job submission is called
fsl_sub_mgh (a modification of fsl_sub).

BTW, the -prior step should be about 70% less long and cumbersome in
5.2/5.3 than it was in 5.1. Which version are you running?

a.y

On Fri, 17 May 2013, Susan Kuo wrote:

> Hi Anastasia,
>   I apologize for jumping in here, but I have run bedpostx parallelized on a
> cluster. Are there files that we can modify to run the script in parallel? I
> noticed the '-prior' step is particularly long and cumbersome. Thank you!
>
>
> Susie Kuo
> NIH
>
>
> On Fri, May 17, 2013 at 12:47 PM, Anastasia Yendiki 
> 
> wrote:
>
>   Hi Matt - Have you ever ran any parallelized FSL program (like
>   bedpostx) on your SGE cluster? Our scripts have built on the FSL
>   scripts, adding support for our PBS cluster, but in theory the SGE
>   functionality is still there, so it should be possible to make it
>   work. Of course practice is often somewhat more complicated than
>   theory...
>
>   a.y
>
>   On Thu, 16 May 2013, Hoptman, Matthew wrote:
>
>
>   Hi all,
>   I have access to a cluster computer.  Is there any way to
>   parallelize tracula
>   using SGE without having to make a unique dmrirc for each
>   subject?  If I could
>   pass subject numbers to the dmrirc that would be great, for
>   example.
>
>   Thanks,
>
>   Matt
>
>
>
>   Matthew J. Hoptman, PhD
>   Research Scientist V
>   Nathan S. Kline Institute for Psychiatric Research
>
>   Research Associate Professor in Psychiatry
>   NYU School of Medicine
>
>
>
>   IMPORTANT NOTICE: This e-mail is meant only for the use of the
>   intended recipient.
>   It may contain confidential information which is legally
>   privileged or otherwise
>   protected by law. If you received this
>   e-mail in error or from someone who was not authorized to send
>   it to you, you are
>   strictly prohibited from reviewing, using, disseminating,
>   distributing or copying
>   the e-mail.
>
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>   DELETE THIS MESSAGE
>   FROM YOUR SYSTEM. Thank you for your cooperation.
>
>
>
> _
> _
> Conserve Resources. Print only when necessary.
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> protected by law. If you received this e-mail in error or from someone
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> ___
> Freesurfer mailing list
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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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>
> Mediocrity knows nothing higher than itself, but talent 

[Freesurfer] FW: Tracula problem

[Hoptman, Matthew]

Hi Anastasia,

I'm just forwarding a modified version of the email I'd sent you earlier to the 
list so everyone can see it.

I solved this particular problem in a new dmrirc, but it seemed that I had to 
modify trac-preproc to remove the ${dcmroot} in front of:
infile, b0mfile and b0pfile:

diff bin/trac-preproc bin/trac-preproc.orig

<   if ($#dcmroot > 0) set infile = $infile
---
>   if ($#dcmroot > 0) set infile = $dcmroot/$infile
259c259
<endif
---
> endif
296c296
< set dcmfile = $b0mfile
---
> set dcmfile = $dcmroot/$b0mfile
311c311
< set dcmfile = $b0pfile
---
> set dcmfile = $dcmroot/$b0pfile

But now it doesn't seem to loop through the subjects, so I'm doing them one at 
a time (painful).

Also, if, as in my other question, I try to run this as a cluster job, I don't 
know how I can substitute a new subject into  subjlist.  I have 64 subjects and 
would like to do trac-all -prep -c dmri on all of them simultaneously.  I have 
used bedpostx in SGE, but there you can just write loop to get it to go through 
your subjects.

If I could make the subject variable external to dmrirc, I could do easily 
script the trac-all job to run in SGE, but I can't fiugre out how to pass it to 
the trac-all command.  Is there any way to pass the subject number directly to 
the command?
Does this make sense?
Matt

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 12:31 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula problem


Hi Matt - Can you source try this on the command line:
source dmrirc_53beta
echo $b0mlist
echo $b0plist

Are these filenames correct, do these files exist? This is how you define
them in your configuration file:
set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`)
set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`)

Thanks,
a.y

On Wed, 15 May 2013, Hoptman, Matthew wrote:

>
> Hi all,
>
>
>
> I’m having a problem with tracula.  I’m trying to run in version 5.3 beta (is 
> that
> version very different from the newer 5.3?).  If I run
>
> trac-preproc   -c dmrirc –prep,
>
>
> I get:
>
> mri_convert /home/hoptman/freesurfer/subjects/c159032/
> /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
>
> mri_convert /home/hoptman/freesurfer/subjects/c159032/
> /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
>
> corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info
>
>
>
> I don’t know why it would look for COR-.info in the subjects’ root directory. 
>  I’m
> attaching my dmrirc file in case that helps.
>
>
>
> Thanks,
> Matt
>
> Matthew J. Hoptman, PhD
> Research Scientist V
> Nathan S. Kline Institute for Psychiatric Research
>
> Research Associate Professor in Psychiatry
> NYU School of Medicine
>
>
>
> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
> recipient.
> It may contain confidential information which is legally privileged or 
> otherwise
> protected by law. If you received this
> e-mail in error or from someone who was not authorized to send it to you, you 
> are
> strictly prohibited from reviewing, using, disseminating, distributing or 
> copying
> the e-mail.
>
> PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
> MESSAGE
> FROM YOUR SYSTEM. Thank you for your cooperation.
>
>
>
> __
> Conserve Resources. Print only when necessary.
>
> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
> recipient.
> It may contain confidential information which is legally privilegedor 
> otherwise
> protected by law. If you received this e-mail in error or from someone who is 
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> you for
> your cooperation.

Re: [Freesurfer] Tracula problem

[Hoptman, Matthew]

Hi Anastasia,
To follow up, yes, those files exist.

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 12:31 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula problem


Hi Matt - Can you source try this on the command line:
source dmrirc_53beta
echo $b0mlist
echo $b0plist

Are these filenames correct, do these files exist? This is how you define
them in your configuration file:
set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`)
set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`)

Thanks,
a.y

On Wed, 15 May 2013, Hoptman, Matthew wrote:

>
> Hi all,
>
>
>
> I’m having a problem with tracula.  I’m trying to run in version 5.3 beta (is 
> that
> version very different from the newer 5.3?).  If I run
>
> trac-preproc   -c dmrirc –prep,
>
>
> I get:
>
> mri_convert /home/hoptman/freesurfer/subjects/c159032/
> /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
>
> mri_convert /home/hoptman/freesurfer/subjects/c159032/
> /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
>
> corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info
>
>
>
> I don’t know why it would look for COR-.info in the subjects’ root directory. 
>  I’m
> attaching my dmrirc file in case that helps.
>
>
>
> Thanks,
> Matt
>
> Matthew J. Hoptman, PhD
> Research Scientist V
> Nathan S. Kline Institute for Psychiatric Research
>
> Research Associate Professor in Psychiatry
> NYU School of Medicine
>
>
>
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[Freesurfer] any way to parallelize Tracula?

[Hoptman, Matthew]

Hi all,
I have access to a cluster computer.  Is there any way to parallelize tracula 
using SGE without having to make a unique dmrirc for each subject?  If I could 
pass subject numbers to the dmrirc that would be great, for example.
Thanks,
Matt

Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine

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[Freesurfer] Tracula problem

[Hoptman, Matthew]

Hi all,

I'm having a problem with tracula.  I'm trying to run in version 5.3 beta (is 
that version very different from the newer 5.3?).  If I run
trac-preproc   -c dmrirc -prep,

I get:
mri_convert /home/hoptman/freesurfer/subjects/c159032/ 
/home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
mri_convert /home/hoptman/freesurfer/subjects/c159032/ 
/home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info

I don't know why it would look for COR-.info in the subjects' root directory.  
I'm attaching my dmrirc file in case that helps.

Thanks,
Matt
Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine

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dmrirc_53beta
Description: dmrirc_53beta
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[Freesurfer] freeview crash

[Hoptman, Matthew]

Hi Ruopeg, 

No, glxgears doesn't crash.  I'm getting about 3929 FPS.

Thanks,

Matt



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[Freesurfer] FW: freeview crash

[Hoptman, Matthew]

Hi all,

I've been using Freesurfer for several years.  I just upgraded to v.
5.1, but when I try to run freeview it crashes.  I am running it on a
64-bit Centos 5.4 server and am accessing the server with Xming.   When
I try to start freeview it crashes Xming and I have to restart it.

 

The only clue I have is when I try freeview.bin, I get "freeview.bin:
error while loading shared libraries: libvtkverdict.so.5.6: cannot open
shared object file: No such file or directory".  I'm wondering if it's a
vtk problem.  

 

Any thoughts?

--Matt



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[Freesurfer] license file

[Hoptman, Matthew]

Hi,

I just registered my new installation of Freesurfer 5.1, but I've used
5.0 and 4.5 in the past.  Can I just copy the ".license" file from the
prior installation?  My impression is I needed a new .license file for
v. 5.1, but I haven't received it despite registering.

--Matt



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[Freesurfer] version number

[Hoptman, Matthew]

Hi, 

I have a relatively old version of Freesurfer, and I'm not sure how to
get the version number.  Could anyone please advise?  It's from back in
the day when we used csurf.

Best,
Matt

 

Matthew J. Hoptman, PhD 
Research Scientist V 
Nathan S. Kline Institute for Psychiatric Research 

Research Associate Professor in Psychiatry 
NYU School of Medicine 

 

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[Freesurfer] how to?

[Hoptman, Matthew]

Hi all,

How do I apply a Talairach registration to a
segmentation?  I can apply the transformation to the main volume and
auxiliary volume in tkmedit, but I am not sure how to apply it to a
segmentation volume.  It looks like I can't load an aseg.mgz file as a
main or auxiliary volume.

--Matt

 

Matthew J. Hoptman, PhD 
Research Scientist V 
Nathan S. Kline Institute for Psychiatric Research 

Research Associate Professor in Psychiatry 
NYU School of Medicine 

 

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[Freesurfer] tksurfer woes

[Hoptman, Matthew]

Hi all,

I'm having trouble using freesurfer's tksurfer program (I only get a
sliver of the brain).  Here is the error info I get:

 

[ghidra: subjects]$ tksurfer 77059 lh pial

surfer: current subjects dir: /home/freesurfer/subjects

surfer: not in "scripts" dir ==> using cwd for session root

surfer: session root data dir ($session) set to:

surfer: /home/freesurfer/subjects

surfer: Reading header info from
/home/freesurfer/subjects/77059/mri/T1.mgz

surfer: vertices=184362, faces=368720

Loading /home/freesurfer/surface_labels.txt

surfer: ### redraw failed: no gl window open

surfer: single buffered window

surfer: tkoInitWindow(77059)

surfer: using interface /home/freesurfer/lib/tcl/tksurfer.tcl

Reading /home/freesurfer/lib/tcl/tkm_common.tcl

Reading /home/freesurfer/lib/tcl/tkm_wrappers.tcl

Reading /home/freesurfer/lib/tcl/fsgdfPlot.tcl

Reading /home/freesurfer/lib/tcl/tkUtils.tcl

Successfully parsed tksurfer.tcl

reading white matter vertex locations...

 

The driver info (from /etc/X11/xorg.conf) is:

Section "Device"

  BoardName"ES1000 515E"

  BusID"14:13:0"

  Driver   "radeon"

  Identifier   "Device[0]"

  Option   "GARTSize" "32"

  Option   "usevnc" "yes"

 

Section "DRI"

Group  "video"

Mode   0660

EndSection

 

 

I'm have an onboard ATI ES1000 515E graphics chip.

 

Any ideas??

Matthew J. Hoptman, PhD 
Research Scientist V 
Nathan S. Kline Institute for Psychiatric Research 

Research Associate Professor in Psychiatry 
NYU School of Medicine 

 



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