Re: [Freesurfer] Error with "recon-all -make all" following multiple manual editing

[Niels Bergsland]

External Email - Use Caution

Hi all,
Just following up on this as I've run into the exact same problem. Is there
a different recon-all.makefile that should be used for FS 6/6.0.1 ?

Thanks!


On Fri, Mar 29, 2019 at 9:28 AM Matthieu VANHOUTTE <
matthieuvanhou...@gmail.com> wrote:

> External Email - Use Caution
>
> Dear Freesurfer's experts,
>
> Havng done multiple types of manual editing in two subjects, I relaunched
> the recon-all process (Freesurfer 6.0.1) with the flag "-make all".
>
> However, during the process, I goth for both subjects the following error
> message:
>
> *make: ***
> [/netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv1s097/mri/aseg.presurf.mgz]
> Error 1*
>
>
> *recon-all -s /netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv3s024
> -ccseg ERROR: Flag -ccseg unrecognized.*
>
> Following the troubleshooting site (
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0)
> I have over-writed the "recon-all.makefile" file since I use the 6.0.1
> version of Freesurfer.
>
> Thanks for helping.
>
> Best,
>
> Matthieu
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Re: [Freesurfer] e-TIV

[Niels Bergsland]

External Email - Use Caution

Hi,
This won't affect the eTIV as that is derived purely from the affine
registration. See Buckner et al. (2004) NeuroImage 23:724-738. for more
details.

-Niels

On Mon, Nov 26, 2018 at 6:46 AM 박경일  wrote:

> External Email - Use Caution
>
> Dear experts,
> When I see the images through freeview to edit, upper brainstem and optic
> chiasm were always included in wm or brainmask.mgz, as an attached picture
> below. Left side seems to be recognized as white matter, and right side as
> cortex. My concern is that this could affect the final value of e-TIV after
> recon-all process, so I need to edit these areas manually.
> I'd appreciated your help. Thanks so much.
>
> Kyung
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Re: [Freesurfer] Longitudinal brainstem structures / thalamic nuclei

[Niels Bergsland]

External Email - Use Caution

Hi Eugenio,
Thanks as always for the speedy response!
I was already going that route just wanted to make sure that something else
wasn’t just around the corner.
Thanks again!
Niels

On Mon, Nov 5, 2018 at 9:44 PM Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> External Email - Use Caution
>
> Hi Niels,
>
> There is, but not in the short term. For the time being, you can run the
> module on longitudinally processed subjects.
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> Centre for Medical Image Computing (CMIC)
>
> Department of Medical Physics and Biomedical Engineering
>
> University College London
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of Niels
> Bergsland 
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, 5 November 2018 at 11:33
> *To: *Freesurfer Mailing List 
> *Subject: *[Freesurfer] Longitudinal brainstem structures / thalamic
> nuclei
>
>
>
> *External Email - Use Caution*
>
> Hi Eugenio,
>
> Just wanted to ask quickly if there is plan to implement longitudinal
> processing for the brainstem structures and thalamic nuclei modules?
>
> Thanks!
>
> Niels
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[Freesurfer] Longitudinal brainstem structures / thalamic nuclei

[Niels Bergsland]

External Email - Use Caution

Hi Eugenio,
Just wanted to ask quickly if there is plan to implement longitudinal
processing for the brainstem structures and thalamic nuclei modules?
Thanks!
Niels
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[Freesurfer] Disjointed thalamic nuclei segmentation

[Niels Bergsland]

External Email - Use Caution

Hi Eugenio,
Thank you again for the fantastic thalamic nuclei segmentation tool!

I'm going through and QC'ing a batch of subjects that were processed
through the pipeline. Data was originally processed with freesurfer-6.0.0
and then processed through the thalamic nuclei stream
(dev-20180818-e30e6f9).

I have found that for some cases, there are some isolated patches of voxels
that are disconnected and seemingly in the wrong place. I've noticed it
primarily for the MDm and my impression is that it tends to happen more in
the right hemisphere. I've attached a sample image to show you what I mean.
The red cross has been placed on a set of these voxels.  It is not the case
that they are connected in 3D.

Any input is appreciated and thanks again! If it can be useful, I'm happy
to upload the data

-Niels
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Re: [Freesurfer] Minimum FS version for thalamic segmentation

[Niels Bergsland]

External Email - Use Caution

Hi Eugenio,
Great - thanks for the quick feedback. Just didn't want to spend the time
recalling things from our longterm storage if it was known be incompatible.

Thanks also for your work on these tools! :)

Best,
Niels

On Wed, Sep 12, 2018 at 4:43 PM Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> External Email - Use Caution
>
> Hi Niels
> 5.1 should do but please let us know if it doesn't!
> Cheers
> E
>
> Sent from my phone, please excuse brevity and typos
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Niels Bergsland <
> theni...@gmail.com>
> *Sent:* Wednesday, September 12, 2018 1:25:18 PM
> *To:* Freesurfer Mailing List
> *Subject:* [Freesurfer] Minimum FS version for thalamic segmentation
>
>
> External Email - Use Caution
>
> Hi Eugenio,
> Just a quick question - is there a minimum version of FS that is required
> to run the thalamic nuclei segmentation? I am just thinking about some old
> datasets that we have that were run with FS 5.1.
> Thanks and best wishes,
> Niels
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[Freesurfer] Minimum FS version for thalamic segmentation

[Niels Bergsland]

External Email - Use Caution

Hi Eugenio,
Just a quick question - is there a minimum version of FS that is required
to run the thalamic nuclei segmentation? I am just thinking about some old
datasets that we have that were run with FS 5.1.
Thanks and best wishes,
Niels
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Re: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error

[Niels Bergsland]

External Email - Use Caution

Hi all,
Not sure if this was resolved off-list or not, but I just ran into it
myself and it turned out to be a permissions-related error in that the user
didn't have read access to some of the required files in the Matlab
runtime. Setting them appropriately resolved the issue.

Best,
Niels

On Thu, Jul 5, 2018 at 9:37 PM Sean Ma  wrote:

> External Email - Use Caution
>
> Hi Eugenio,
>
> Thanks for the tip.
>
> I've deleted the /MCR* folder in /tmp and made sure I had enough space in
> /tmp - 9GB.
>
> Unfortunately, the same error message still exists.
>
> Let me know if I could further send any debugging logs to help isolate
> this issue.
>
> Thanks for your help!
>
>
> Best,
>
> Sean
> University of Michigan
>
>
>
> On Tue, Jul 3, 2018 at 5:59 AM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
>> External Email - Use Caution
>>
>> I was thinking it could be a corrupt MCR cache. Could you please:
>>
>> a) Delete /tmp/MCR* directories
>>
>> b) Make sure you've got enough space in /tmp/
>>
>> Cheers,
>>
>> /Eugenio
>>
>>
>> Juan Eugenio Iglesias
>>
>> Centre for Medical Image Computing (CMIC)
>>
>> University College London
>>
>> http://www.jeiglesias.com
>>
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sean Ma <
>> tehsh...@umich.edu>
>> *Sent:* Tuesday, July 3, 2018 1:43:18 AM
>> *To:* Freesurfer support list
>> *Cc:* Hoopes, Andrew
>> *Subject:* Re: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield
>> Matlab runtime Java error
>>
>>
>> External Email - Use Caution
>>
>> Hi Eugenio,
>>
>> I’ve followed the wiki and installed it based on the instructions. My
>> server runs on RHEL7.
>>
>> Best,
>>
>> Sean
>>
>>
>>
>> On Mon, Jul 2, 2018 at 3:47 PM Iglesias Gonzalez, Eugenio <
>> e.igles...@ucl.ac.uk> wrote:
>>
>> External Email - Use Caution
>>
>> That’s rather ugly.
>>
>> Sean: did you install the runtime from the Mathworks website, or did you
>> download / uncompress following the instrucitons in the wiki?
>>
>> Andrew:  any ideas?
>>
>> Cheers,
>>
>> /Eugenio
>>
>>
>>
>> --
>>
>> Juan Eugenio Iglesias
>>
>> ERC Senior Research Fellow
>>
>> Centre for Medical Image Computing (CMIC)
>>
>> University College London
>>
>> http://www.jeiglesias.com
>>
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>>
>>
>>
>> *From: * on behalf of Sean Ma <
>> tehsh...@umich.edu>
>> *Reply-To: *Freesurfer support list 
>> *Date: *Monday, 2 July 2018 at 20:33
>> *To: *"freesurfer@nmr.mgh.harvard.edu" 
>> *Subject: *[Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield
>> Matlab runtime Java error
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Eugenio,
>>
>>
>>
>> I'd like to report a Matlab runtime Java error when running the
>> Hippocampal subfield on FS6.0-dev (Jun 27, 2018) after a successful
>> completion of `recon-all`. Matlab 2014b runtime has been successfully
>> expanded at /MCRv84.
>>
>>
>>
>> The error I've encountered follows. Any suggestions on how I can overcome
>> this error?
>>
>>
>>
>> Thanks for your pointers!
>>
>>
>>
>> Best,
>>
>>
>>
>> Sean Ma
>>
>> University of Michigan
>>
>>
>>
>> ==
>>
>>
>>
>> [tehsheng@b-fmri FS6results]$ segmentHA_T1.sh b30002_02712
>>
>> #
>>
>> #@# Hippocampal Subfields processing (T1) left Mon Jul  2 15:16:41 EDT
>> 2018
>>
>> --
>>
>> Setting up environment variables
>>
>> ---
>>
>> LD_LIBRARY_PATH is
>> .:/opt/freesurfer6/MCRv84//runtime/glnxa64:/opt/freesurfer6/MCRv84//bin/glnxa64:/opt/freesurfer6/MCRv84//sys/os/glnxa64::/opt/freesurfer6/MCRv84//sys/opengl/lib/glnxa64:
>>
>> Error using checkRequiredMCRProducts (line 25)
>>
>> Java exception occurred:
>>
>> java.lang.NullPointerException
>>
>> at
>> com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)
>>
>> at
>> com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)
>>
>> at
>> com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)
>>
>> at
>> com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)
>>
>> at
>> com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)
>>
>>
>>
>> Error in deployrc (line 9)
>>
>>
>>
>> Error in matlabrc (line 238)
>>
>>
>>
>>
>>
>> @#@FSTIME  2018:07:02:15:16:41
>> run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 32.59 S 0.39 U 5.00 P
>> 16% M 205368 F 82 R 43627 W 0 c 54 w 1963 I 24008 O 82888 L 0.00 0.07 0.89
>>
>> @#@FSLOADPOST 2018:07:02:15:17:13
>> run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.15 0.11 0.87
>>
>> Linux b-fmri.edu 2.6.32-696.28.1.el6.x86_64 #1 SMP 

Re: [Freesurfer] mri_segment error

[Niels Bergsland]

Your input here is a localizer image:

Protocol  t2_haste_localizer_p2



On Mon, Mar 19, 2018 at 12:51 PM, Z Hessam  wrote:
>
> hello, i have problem again with a new data set.
> this is the recon-all.log file in attach
>
> thanks a lot
>
>
> On Fri, Feb 9, 2018 at 2:22 PM, Z Hessam  wrote:
>>
>> thank you for your attention
>>
>> regards
>>
>> On Fri, Feb 9, 2018 at 1:04 AM, Bruce Fischl 
wrote:
>>>
>>> looks like the acquisition is not what you would need to run FreeSurfer
on. Looking at the log I think your input is a T2-weighted image (we
require a T1) with a slice thickness of 9mm (we require all voxel
dimensions to be <=1.5mm or so)
>>>
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>>
>>> On Thu, 8 Feb 2018, Z Hessam wrote:
>>>
 sure...
 with first code i convert *.dcm files.
 with second code i want to segment data:

 1) recon-all -i /media/hessam91/driver2/data/1.dcm -autorecon1 -subjid
dyegmoh
 2) recon-all -s dyegmoh -all

 and the log file is attached(recon-all_dyegmoh.log).




 On Thu, Feb 8, 2018 at 7:05 PM, Bruce Fischl <
fis...@nmr.mgh.harvard.edu> wrote:
   can you send us the complete command you ran, the entire screen
output and the
   recon-all.log file?

   cheers
   Bruce
   On Thu, 8 Feb 2018, Z Hessam wrote:

 Hello FreeSurfer develpers
 I'm attempting to run " recon-all " command on a file of
dicom data, and
 encounter with an error
 command:

 recon-all -s dyegmoh exited with ERRORS  at Thu Feb  8
17:08:16 +0330 2018

 how can i understand why this error happens  and what
should i do to solve
 it?




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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
>>> 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] Difficulties running tracula

[Niels Bergsland]

Hi again,
The latest version is 5.0.10 but the issue was definitely fixed in 5.0.9
(possibly one point release earlier, I can't recall). Regardless, I don't
think there were any changes to flirt between 5.0.9 and 5.0.10.

Good luck!
Niels

On Fri, Feb 16, 2018 at 5:40 PM, John Davis  wrote:

> Anastasia,
> Great - this is awesome (knock on wood). Version 5.0.9 looks stable, but I
> should probably ask IT department for the recommended. Is that the latest
> stable version?
> John
>
> On Fri, Feb 16, 2018 at 8:56 AM, Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> OK, so the ones that come from bbregister (a freesurfer tool) are fine.
>> Then it's possible that this is related to the FSL glitch. It's worth
>> trying. Sorry about this, I hope to reduce dependencies in the future.
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of John Davis <
>> jda...@mrn.org>
>> *Sent:* Friday, February 16, 2018 10:39:35 AM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Difficulties running tracula
>>
>> Anastasia,
>> Q: Do the other registration files look like this too?
>> I'm glad you asked. I looked at the .mat files. Two of the mat files have
>> regular numbers. The rest have hex. Also, many of the numbers in these
>> files seem quite huge to me. The two mat files that look normal are
>> anatorig2anat.mat and diff2anatorig.bbr.mat. I put some examples, including
>> both hex and regular, in the attachment. I also put ".dat" and ".dat.sum".
>> Those look normal, too.
>>
>> Also, Anastasia and Niels, the two most recent we have are fsl-5.0.1 and
>> fsl-5.0.5. I set $FSLDIR to fsl-5.0.1.
>>
>> Once again thanks.
>> John
>>
>> On Thu, Feb 15, 2018 at 6:10 PM, Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>> Sorry to hear. Do the other registration files in the dmri/xmfs/
>> directory, including diff2anatorig.bbr.mat, look like this too?
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of John Davis <
>> jda...@mrn.org>
>> *Sent:* Thursday, February 15, 2018 4:47:39 PM
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Difficulties running tracula
>>
>> Anastasia,
>> I tried your solution.
>> "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files.
>> Unfortunately, it didn't work. I did it from both a tcsh and a bash
>> shell. (local reasons for trying that). Neither worked. The outcome was
>> identical, but I can send the files in again if you need.
>> Thank you for helping
>> John
>>
>> On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>> Hi John – The problem is the funky format of the numbers in that
>> registration file. It expects a 4x4 matrix of regular decimal numbers. Are
>> the numbers in all the other registration files in the xfms/ directory in
>> this same format? It probably has something to do with how your unix
>> environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does
>> this change the output?
>>
>> Best,
>> a.y
>>
>> From:  on behalf of John Davis <
>> jda...@mrn.org>
>> Reply-To: Freesurfer support list 
>> Date: Monday, February 12, 2018 at 11:20 AM
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Subject: [Freesurfer] Difficulties running tracula
>>
>> The information you request is in the attachments. Also I sent dmrirc.
>>
>> --
>> John Davis, PhD
>> Cell: (520) 907-9769
>> jda...@mrn.org
>>
>> ___
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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.
>>
>>
>>
>>
>> --
>> John Davis, PhD
>> Cell: (520) 907-9769
>> jda...@mrn.org
>>
>> ___
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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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>> in error
>> but does not contain patient information, please contact the sender and
>> 

Re: [Freesurfer] Difficulties running tracula

[Niels Bergsland]

Hi Anastasia and John,
This looks like the glibc issue that was fixed in more recent versions of
FSL. Given that you are running Ubuntu 16.04, if you are using an older
version of FSL, you will get FLIRT matrices saved in hexadecimal format. If
you upgrade your FSL to a more recent version, you should be okay.

On Fri, Feb 16, 2018 at 2:10 AM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> Sorry to hear. Do the other registration files in the dmri/xmfs/
> directory, including diff2anatorig.bbr.mat, look like this too?
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of John Davis <
> jda...@mrn.org>
> *Sent:* Thursday, February 15, 2018 4:47:39 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Difficulties running tracula
>
> Anastasia,
> I tried your solution.
> "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files.
> Unfortunately, it didn't work. I did it from both a tcsh and a bash shell.
> (local reasons for trying that). Neither worked. The outcome was identical,
> but I can send the files in again if you need.
> Thank you for helping
> John
>
> On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi John – The problem is the funky format of the numbers in that
> registration file. It expects a 4x4 matrix of regular decimal numbers. Are
> the numbers in all the other registration files in the xfms/ directory in
> this same format? It probably has something to do with how your unix
> environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does
> this change the output?
>
> Best,
> a.y
>
> From:  on behalf of John Davis <
> jda...@mrn.org>
> Reply-To: Freesurfer support list 
> Date: Monday, February 12, 2018 at 11:20 AM
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Subject: [Freesurfer] Difficulties running tracula
>
> The information you request is in the attachments. Also I sent dmrirc.
>
> --
> John Davis, PhD
> Cell: (520) 907-9769
> jda...@mrn.org
>
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>
>
>
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> Cell: (520) 907-9769
> jda...@mrn.org
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Re: [Freesurfer] recon-all base error

[Niels Bergsland]

Hi - how much memory do you have on your machine?

On Mon, Dec 14, 2015 at 10:54 AM, salvatoreandrea...@libero.it <
salvatoreandrea...@libero.it> wrote:

> Hi Freesurfer experts!
>
> I tried to run recon-all base for a longitudinal analysis on my data. But
> I get the following error:
>
>
>
> *Excessive topologic defect encountered: could not allocate 221309241 edges 
> for retessellationCannot allocate memoryLinux salvatore-HP-630-Notebook-PC 
> 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 
> x86_64 x86_64 GNU/Linux*
>
> I tried with a more powerful pc but I encountered the same problem.
>
> Following further information:
>
> SUBJECT template_base
> DATE ven 11 dic 2015, 08.17.47, CET
> USER salvatore
> HOST salvatore-HP-630-Notebook-PC
> PROCESSOR x86_64
> OS Linux
> Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu
> SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
> /home/salvatore/freesurfer/bin/recon-all
> PWD /home/salvatore/freesurfer/subjects/template_base/scripts
> CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234
> template_base lh
>
>
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Re: [Freesurfer] R: Re: report a bug

[Niels Bergsland]

Hi - that's way too low, unfortunately. You need at least 4GB and more is
preferred.

See: https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements


On Mon, Nov 30, 2015 at 5:19 PM, salvatoreandrea...@libero.it <
salvatoreandrea...@libero.it> wrote:

> I have around 2 Gb of total RAM. Isn't that sufficient to run recon-all?
> If it is not, do you know whether there is a way to split up the process?
>
>
> Messaggio originale
> Da: theni...@gmail.com
> Data: 27-nov-2015 17.24
> A: "salvatoreandrea...@libero.it",
> "Freesurfer support list"
> Ogg: Re: [Freesurfer] report a bug
>
>
> Hi - sounds like it's running out of memory and getting killed. How much
> RAM do you have?
>
> On Thu, Nov 26, 2015 at 1:21 PM, salvatoreandrea...@libero.it <
> salvatoreandrea...@libero.it> wrote:
>
>> Hi!
>> - I am using Ubuntu 14.4 (trusty).
>>
>> -  This is my subject directory: /home/salvatore/freesurfer/subjects
>>
>> - This is the output of *which recon-all *(that is the tool I am trying
>> to use): /home/salvatore/freesurfer/bin/recon-all
>>
>> - The command line that I run is
>>
>> *recon-all -s /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis
>> -i /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis/T1.nii.gz
>> -all*Following the error that I got after 12 hours of processing:
>>
>>
>> sysname  Linux
>> hostname salvatore-HP-630-Notebook-PC
>> machine  x86_64
>>
>> setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects
>> cd /home/salvatore/freesurfer/subjects/FreeSurfer_analysis/mri
>> mri_ca_label -align norm.mgz transforms/talairach.m3z
>> /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca
>> aseg.auto_noCCseg.mgz
>>
>> renormalizing sequences with structure alignment, equivalent to:
>> -renormalize
>> -renormalize_mean 0.500
>> -regularize 0.500
>> reading 1 input volumes...
>> reading classifier array from
>> /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca...
>> reading input volume from norm.mgz...
>> Killed
>> Linux salvatore-HP-630-Notebook-PC 3.19.0-33-generic #38~14.04.1-Ubuntu
>> SMP Fri Nov 6 18:17:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s FreeSurfer_analysis exited with ERRORS at gio 26 nov 2015,
>> 12.42.40, CET
>>
>>
>> Could you please help me to fix this problem? I tried to ran it again in
>> an other terminal, without succeding...Thank you
>>
>>
>> Best,
>>
>> Salvatore
>>
>>
>>
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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] report a bug

[Niels Bergsland]

Hi - sounds like it's running out of memory and getting killed. How much
RAM do you have?

On Thu, Nov 26, 2015 at 1:21 PM, salvatoreandrea...@libero.it <
salvatoreandrea...@libero.it> wrote:

> Hi!
> - I am using Ubuntu 14.4 (trusty).
>
> -  This is my subject directory: /home/salvatore/freesurfer/subjects
>
> - This is the output of *which recon-all *(that is the tool I am trying
> to use): /home/salvatore/freesurfer/bin/recon-all
>
> - The command line that I run is
>
> *recon-all -s /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis
> -i /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis/T1.nii.gz
> -all*Following the error that I got after 12 hours of processing:
>
>
> sysname  Linux
> hostname salvatore-HP-630-Notebook-PC
> machine  x86_64
>
> setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects
> cd /home/salvatore/freesurfer/subjects/FreeSurfer_analysis/mri
> mri_ca_label -align norm.mgz transforms/talairach.m3z
> /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca
> aseg.auto_noCCseg.mgz
>
> renormalizing sequences with structure alignment, equivalent to:
> -renormalize
> -renormalize_mean 0.500
> -regularize 0.500
> reading 1 input volumes...
> reading classifier array from
> /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca...
> reading input volume from norm.mgz...
> Killed
> Linux salvatore-HP-630-Notebook-PC 3.19.0-33-generic #38~14.04.1-Ubuntu
> SMP Fri Nov 6 18:17:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s FreeSurfer_analysis exited with ERRORS at gio 26 nov 2015,
> 12.42.40, CET
>
>
> Could you please help me to fix this problem? I tried to ran it again in
> an other terminal, without succeding...Thank you
>
>
> Best,
>
> Salvatore
>
>
>
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Re: [Freesurfer] White matter and pial surfaces not tracking sulcus

[Niels Bergsland]

Hi all,
Sorry for the repost, was just wondering whether someone might have some
input regarding this issue.

Thanks!
Niels

On Thu, Mar 26, 2015 at 12:10 PM, Niels Bergsland theni...@gmail.com
wrote:

 Hi all,
 I have run into an issue that I am having trouble correcting.

 http://imgur.com/a/4KqpJ

 I have checked the aseg to see if it was labeled as ventricle. This does
 not seem to be the cause.

 Any other suggestions? I am happy to upload the case if that is necessary.

 Best regards,
 Niels




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[Freesurfer] White matter and pial surfaces not tracking sulcus

[Niels Bergsland]

Hi all,
I have run into an issue that I am having trouble correcting.

http://imgur.com/a/4KqpJ

I have checked the aseg to see if it was labeled as ventricle. This does
not seem to be the cause.

Any other suggestions? I am happy to upload the case if that is necessary.

Best regards,
Niels
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[Freesurfer] mri_convert on 64bit vs 32bit

[Niels Bergsland]

Hi,
I am experiencing quite a strange problem.  I have a set of DICOMs
that when I run the following on a 32bit machine, it works fine:
mri_convert 031G0110.101.dcm 001.mgz

When I run the exact same command (from within the same directory) on
the 64 bit machine, I get the following error:
Currently non-Siemens mosaic image cannot be handled.  Exit

(I should note that these are not actually mosaic images, they are individual)

mri_convert --all-info on the 32 bit machine yields the following:
mri_convert --all-info
ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion:
$Name: stable3 $ TimeStamp: 06/10/12-20:37:40-GMT CVS: $Id:
mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: niels
Machine: freya.bnac Platform: Linux PlatformVersion:
2.6.9-42.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400

and on the 64 bit machine:

mri_convert --all-info
ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion:
$Name: stable3 $ TimeStamp: 06/10/12-20:38:29-GMT CVS: $Id:
mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: niels
Machine: giza Platform: Linux PlatformVersion: 2.6.9-22.ELsmp
CompilerName: GCC CompilerVersion: 30400

We have used the 64 bit install extensively before and never run into
this issue.
Any insight?
Thanks!
Regards,
Niels Bergsland
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Re: [Freesurfer] mri_convert on 64bit vs 32bit

[Niels Bergsland]

Hi Nick,
Thanks for the response.  They are from a Philips machine though...
Niels

On 10/12/06, Nick Schmansky [EMAIL PROTECTED] wrote:

Niels,

Are they Siemens Dicom files?  If so, try adding the flag -siemens_dicom
to mri_convert.

This wouldn't explain the difference in behavior between the 32bit and
64bit builds though.  I have not personally encountered the message you
are seeing.

Nick

On Thu, 2006-10-12 at 16:40 -0400, Niels Bergsland wrote:
 Hi,
 I am experiencing quite a strange problem.  I have a set of DICOMs
 that when I run the following on a 32bit machine, it works fine:
 mri_convert 031G0110.101.dcm 001.mgz

 When I run the exact same command (from within the same directory) on
 the 64 bit machine, I get the following error:
 Currently non-Siemens mosaic image cannot be handled.  Exit

 (I should note that these are not actually mosaic images, they are individual)

 mri_convert --all-info on the 32 bit machine yields the following:
 mri_convert --all-info
 ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion:
 $Name: stable3 $ TimeStamp: 06/10/12-20:37:40-GMT CVS: $Id:
 mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: niels
 Machine: freya.bnac Platform: Linux PlatformVersion:
 2.6.9-42.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400

 and on the 64 bit machine:

 mri_convert --all-info
 ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion:
 $Name: stable3 $ TimeStamp: 06/10/12-20:38:29-GMT CVS: $Id:
 mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: niels
 Machine: giza Platform: Linux PlatformVersion: 2.6.9-22.ELsmp
 CompilerName: GCC CompilerVersion: 30400

 We have used the 64 bit install extensively before and never run into
 this issue.
 Any insight?
 Thanks!
 Regards,
 Niels Bergsland
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[Freesurfer] Missing Dicom Fields (Revisted)

[Niels Bergsland]

Hi again,

From the last time that I asked about this, the project was

temporarily put on hold, but now it has started up again...

When looking back at the responses from last time, I realized that I
am not sure if I made it clear what I was proposing as a solution to
the missing fields 0020,0032 (ImagePositionPatient) and 0020,0037
(ImageOrientationPatient).
My original question was as follows:

Is it possible to 'fake' the 20,37 field by
inserting the values: 1\0\0\0\1\0   since we know they are acquired in
the axial plane?  We also know which way the
slices are supposed to be sorted, is it possible to insert values into
20,32 in order to have freesurfer able to 'know' the proper sorting
order?

To which you said that you didn't have something to allow us to
specify the fields ourselves.  I realized that you thought I was
asking if Freesurfer has the capability.  What I actually meant though
is if I can manually insert the values using, for example, dcmodify
(part of the DCMTK) and then process the scans with Freesurfer.
Hopefully this is a bit more clear!
Thanks again,
Niels Bergsland
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[Freesurfer] Re: Missing Dicom Fields (Revisted)

[Niels Bergsland]

Hi Doug,
Thanks for the response.  The issue is that the fields are missing,
but we know that the scans are acquired in the axial plane.  Would it
be a horrible idea to insert into 20,37 the following values since
they correspond to a 'true' axial plane: 1\0\0\0\1\0 ?  You mentioned
before that Freesurfer uses 20,32 to calculate the order of the
slices.  Can we insert values into 20,32 in order to allow Freesurfer
to work?  (This would all be done prior to actually using Freesurfer
by using dcmodify from the DCMTK package to manually insert the
values, if this approach is feasible).
Thanks again Doug.
Regards,
Niels

On 10/3/06, Doug Greve [EMAIL PROTECTED] wrote:

Hi Niels,

I can't remember what the original problem was. Were the dicom fields
missing or were they just wrong? We can handle wrong ones, but missing
ones cause our 3rd party dicom reader to fail, which we can't really do
anything about.

doug

Niels Bergsland wrote:

 Hi again,
 From the last time that I asked about this, the project was
 temporarily put on hold, but now it has started up again...

 When looking back at the responses from last time, I realized that I
 am not sure if I made it clear what I was proposing as a solution to
 the missing fields 0020,0032 (ImagePositionPatient) and 0020,0037
 (ImageOrientationPatient).
 My original question was as follows:

 Is it possible to 'fake' the 20,37 field by
 inserting the values: 1\0\0\0\1\0   since we know they are acquired in
 the axial plane?  We also know which way the
 slices are supposed to be sorted, is it possible to insert values into
 20,32 in order to have freesurfer able to 'know' the proper sorting
 order?

 To which you said that you didn't have something to allow us to
 specify the fields ourselves.  I realized that you thought I was
 asking if Freesurfer has the capability.  What I actually meant though
 is if I can manually insert the values using, for example, dcmodify
 (part of the DCMTK) and then process the scans with Freesurfer.
 Hopefully this is a bit more clear!
 Thanks again,
 Niels Bergsland



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting




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Re: [Freesurfer] Regarding missing DICOM fields

[Niels Bergsland]

Hi Doug,
Thanks for the quick response.  These are for single images.  These
older files are missing 0020,0032 (ImagePositionPatient) and 0020,0037
(ImageOrientationPatient).  It is my understanding that 20,37 is used
to establish the direction cosines.  The scans were all acquired in
the axial plane.  Is it possible to 'fake' the 20,37 field by
inserting the values: 1\0\0\0\1\0   ?  We also know which way the
slices are supposed to be sorted, is it possible to insert values into
20,32 in order to have freesurfer able to 'know' the proper sorting
order?
As I said in my first email, I am afraid not... But I figured it would
not hurt to ask.
Thanks!
Cheers,
Niels

On 8/28/06, Doug Greve [EMAIL PROTECTED] wrote:

Which diom tags do you mean? I think we can get away with not having the
Patient Orientation (tag 20,20) -- I'm not sure why I required it in the
first place. ImagePositionPatient (tag 20,32) is considerably more
important as this is one of the ways the slices are sorted and the
direction cosines estabilished. Are these for mosaics?

doug

Niels Bergsland wrote:

 Hi,
 We have some old scans that were originally in ACR-NEMA format which
 we have converted to DICOM.  The problem is that they are missing both
 the ImagePositionPatient and ImageOrientationPatient fields.  Is
 there anyway to use freesurfer without having these two fields?  Based
 on the post by Doug which I found at
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html
 , I am afraid not...

 Thank you for any help.
 Regards,
 Niels Bergsland
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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Regarding missing DICOM fields

[Niels Bergsland]

Thanks for the help Doug!
I will let you know how it goes.

Niels

On 8/29/06, Doug Greve [EMAIL PROTECTED] wrote:

No, I don't have anything which allows you to specify them yourself. On
the other hand, you can work-around this with something like:

mri_probedicom --i slice1.dcm --o slice1.dat

slice1.dat will be a binary file of the pixel data from the file
slice1.dcm. You can do this for each slice, then assemble the data into
a real format. Not fun, but possible. Other tools out there might not
require the direction cosines.

doug

Niels Bergsland wrote:

 Hi Doug,
 Thanks for the quick response.  These are for single images.  These
 older files are missing 0020,0032 (ImagePositionPatient) and 0020,0037
 (ImageOrientationPatient).  It is my understanding that 20,37 is used
 to establish the direction cosines.  The scans were all acquired in
 the axial plane.  Is it possible to 'fake' the 20,37 field by
 inserting the values: 1\0\0\0\1\0   ?  We also know which way the
 slices are supposed to be sorted, is it possible to insert values into
 20,32 in order to have freesurfer able to 'know' the proper sorting
 order?
 As I said in my first email, I am afraid not... But I figured it would
 not hurt to ask.
 Thanks!
 Cheers,
 Niels

 On 8/28/06, Doug Greve [EMAIL PROTECTED] wrote:

 Which diom tags do you mean? I think we can get away with not having the
 Patient Orientation (tag 20,20) -- I'm not sure why I required it in the
 first place. ImagePositionPatient (tag 20,32) is considerably more
 important as this is one of the ways the slices are sorted and the
 direction cosines estabilished. Are these for mosaics?

 doug

 Niels Bergsland wrote:

  Hi,
  We have some old scans that were originally in ACR-NEMA format which
  we have converted to DICOM.  The problem is that they are missing both
  the ImagePositionPatient and ImageOrientationPatient fields.  Is
  there anyway to use freesurfer without having these two fields?  Based
  on the post by Doug which I found at
 
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html
  , I am afraid not...
 
  Thank you for any help.
  Regards,
  Niels Bergsland
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 [EMAIL PROTECTED]
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 In order to help us help you, please follow the steps in:
 surfer.nmr.mgh.harvard.edu/fswiki/BugReporting






--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting




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