date:20190623

[Freesurfer] I have a question for "matlabruntime"

2019-06-23 Thread Gwang-Won Kim

External Email - Use CautionDear there, I tried to process “Segmentation of thalamic nuclei” using source the FreeSurfer development version(freesurfer-linux-centos6_x86_64-dev.tar.gz).The OS of my notebook CentOS (6.10).MATLAB --> /usr/local/MATLAB/R2017bMRCv84 --> /usr/local/freesurfer/MCRv84I filled out “segmentThalamicNuclei.sh  bert  [SUBJECTS_DIR].In my notebook, there was the message such as attached file.Best,













--
USER GW
HOST gwkim
PROCESSID 4990 
PROCESSOR x86_64
OS Linux
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 
Linux gwkim 2.6.32-754.14.2.el6.x86_64 #1 SMP Tue May 14 19:35:42 UTC 2019 
x86_64 x86_64 x86_64 GNU/Linux
--
freesurfer-local-build-dev-20190621
 
setenv SUBJECTS_DIR /home/GW/test
cd /home/GW/test/002_T1T2_Hippo
/usr/local/freesurfer/bin/segmentThalamicNuclei.sh 002_T1T2_Hippo

#
#@# Thalamic Nuclei processing 2019. 06. 23. (ì¼) 23:55:32 KST
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/lib64:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libmwservices.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libmwctfpackage.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_date_time.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_thread.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libut.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libmwfl.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libmwmlutil.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libmwsettingscore.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libmwms.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libmwopccore.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libmwopcmodel.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libmwopczippackage.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libmwopcmwservices.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_serialization.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_log.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_log_setup.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by 
/usr/local/freesurfer/MCRv84//bin/glnxa64/libPocoFoundation.so.21)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/li

[Freesurfer] (no subject)

2019-06-23 Thread fsbuild

External Email - Use Caution

Hello John,



You might be able to tell from the log what directory recon-all was cd'd
 into when the creation of the soft link failed.  You could try to cd 
there as your userid (which I assume you used to run recon-all), and see
 if you can manually create any soft link there.  if you cannot do so, 
there could be a problem with the directory permissions.  The uersid 
running recon-all should have permission to read, write, and execute on 
subdirectories which typically means the permission on them is
 set to be 755.



While do not officially support cuda, I would first check to see you 
have the cuda libraries installed on you system.  You could do a search 
under /usr to see if you have it, e.g.

$ sudo find /usr -name "libcudart*"



- or with the package tools, look to see if any nvidia or cuda packages are 
installed,  e.g.,

$ rpm -qa | grep -i nvid

$ rpm -qa | grep -i cuda



If you don't find a libcudart.so.5 installed, then I think you will need
 to install rev 7.5 of the cuda tools on your system as that should be 
the version with libcudart.so.5



- R.






John AbsherJune 22, 2019 at 22:28
  External Email - Use Caution

Hi, I am testing a new installation of freesurfer. Two errors occurred, and I'm 
hoping someone can help me troubleshoot:

First, recon-all exits with error indicating that it is unable to create a 
symbolic link:

[GHS\026278@vmcntdsktp10 fs_sample1]$ tail 
/neuro_images_isilon/026278/fs_sample1/sample001/scripts/recon-all.log
ICI = 216.7, FI = 1989.1, variation=32373.324
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
Linux vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 
2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sample001 exited with ERRORS at Sat Jun 22 17:10:41 EDT 2019

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The error occurs in CentOS 7 running on a virtual machine environment, with the 
latest stable freesurfer release, 6.0. 

The recon-all process was being run on the sample_001.mgz file to test the 
installation, and ran for about 7 hours.

Second, when I tried to use the -use-gpu flag, the process seems to be missing 
a library:

[GHS\026278@vmcntdsktp10 fs_sample1]$ recon-all -subject sample001 -i 
./sample-001.mgz -use-gpu -all
Testing for CUDA device:
/usr/local/freesurfer/bin/mri_em_register_cuda:
 error while loading shared libraries: libcudart.so.5.0: cannot open 
shared object file: No such file or directory
Linux vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 
2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sample001 exited with ERRORS at Sat Jun 22 10:05:12 EDT 2019

For more details, see the log file 
To report a problem, see http://surfer.nmr.mgh..harvard.edu/fswiki/BugReporting

[GHS\026278@vmcntdsktp10 fs_sample1]$

Can you suggest workarounds for one or both of these errors? Thanks,

John


Warm regards, 


Please, note my new email address, john.abs...@prismahealth.org

John R. Absher, MD, FAAN
Division of Neurology, Department of Medicine

Prisma Health-Upstate 
200 Patewood Drive, Suite 350B
City, SC 29615
864-454-4500 (office)
864-350-6655 (mobile)
864-454-4505 (fax)



Inspire health. Serve with compassion. Be the difference.




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Re: [Freesurfer] voxel coordinates of corpus collosum

2019-06-23 Thread Sadia Sheikh

External Email - Use Caution

I tried to extract cc labels from aseg.auto.mgz file and extract the labels
subregions of cc from the cc.mgz file (cc.mgz contain the segmented
subregions of corpus callosum) using mri_vol2label command.

On Fri, Jun 21, 2019 at 11:23 PM Bruce Fischl 
wrote:

> can you send us the full command line and screen output? Doug might have
> an easy way to do it, but personally I would do it in matlab
> cheers
> Bruce
> On Fri, 21 Jun
> 2019, Sadia Sheikh wrote:
>
> >
> > External Email - Use Caution
> >
> > Thanks for your reply. I want to get the voxel coordinates of  CC and
> its subregions. I tried using
> > the command mri_vol2label for cc subregions also. But still I am getting
> the error message: found no
> > voxels matching id 251.
> > What is the right command to get the coordinates of CC?
> >
> > Thanks in advance.
> > Sadia
> >
> >
> > On Thu, Jun 20, 2019 at 11:08 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   Hi Sadia
> >
> >   we subdivide the cc into multiple components:
> >
> >   251 CC_Posterior0   0   64  0
> >   252 CC_Mid_Posterior0   0   112 0
> >   253 CC_Central  0   0   160 0
> >   254 CC_Mid_Anterior 0   0   208 0
> >   255 CC_Anterior 0   0   255 0
> >
> >
> >   cheers
> >   Bruce
> >
> >   On Thu, 20 Jun
> >   2019, Sadia
> >   Sheikh wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Dear Freesurfer experts
> >   > How can I get the voxel coordinates of the segmented corpus
> callosum? I tried using
> >   the command
> >   > mri_vol2label and id of the corpus callosum as 192  as given in
> Freesurfer LUT,
> >   > but it gives an error: found no voxels matching id 192
> >   >
> >   > Thanks in advance
> >   >
> >   > Sadia
> >   >
> >   >___
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> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
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Re: [Freesurfer] question for preprocessing

2019-06-23 Thread Bruce Fischl

well, we don't run only those steps to generate any volume. Probably your 
best bet would be the norm.mgz, although as Doug says it will have a 
cerebellum in it, which you can strip with the aseg.mgz


cheers
Bruce



On Sun, 23 Jun 2019, ping cao wrote:



External Email - Use Caution

Thank you for your reply.I also want to know which file has just finished with 
1-3 steps?
Is it nu.mgz? Or nu.mgz?
T1.mgz                                   aseg.presurf.mgz           
        
aparc+aseg.mgz                     brain.finalsurfs.mgz             
  
 norm.mgz                                

aparc.DKTatlas+aseg.mgz     brain.mgz                               
 nu.mgz 
                                  aparc.a2009s+aseg.mgz       
brainmask.auto.mgz                                                

aseg.auto.mgz                        brainmask.mgz                  
   
 orig.mgz                                  ctrl_pts.mgz             
        
       orig_nu.mgz                 

wm.asegedit.mgz                    aseg.auto_noCCseg.mgz       
filled.mgz   
                            rawavg.mgz                             
wm.mgz

aseg.mgz                                lh.ribbon.mgz               
        
 rh.ribbon.mgz                         wm.seg.mgz                   
        
  aseg.presurf.hypos.mgz            

ribbon.mgz                           wmparc.mgz


Best,
ping

Greve, Douglas N.,Ph.D.  于2019年6月23日周日 下午9:35写道：
  It does 1-3. It also labels cerebellum which you could then use to 
perform #4

  On 6/23/2019 7:03 AM, ping cao wrote:

  External Email - Use Caution

  Dear expert，
  Thank you for reading!

  I want to do these four pre-processing steps: 

1. Re-sampling each MR image to 256*256*256; 
2. Using the N3 algorithm for intensity inhomogeneity correction;

3. Skull stripping;

4. Removing the cerebellum.

  Does " recon-all"  do all the above 4 steps automatically? If so, which 
file
  is just finished with these four steps? If not, how can I do these steps?

Your help is greatly appreciated.  


Best,
ping

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Re: [Freesurfer] question for preprocessing

2019-06-23 Thread ping cao

External Email - Use Caution

Thank you for your reply.
I also want to know which file has just finished with 1-3 steps?
Is it nu.mgz? Or nu.mgz?

*T1.mgz*   aseg.presurf.mgz
> aparc+aseg.mgz brain.finalsurfs.mgz* 
> norm.mgz
>  *

aparc.DKTatlas+aseg.mgz *brain.mgz  *
> *nu.mgz*aparc.a2009s+aseg.mgz
> brainmask.auto.mgz

aseg.auto.mgzbrainmask.mgz
> *orig.mgz * ctrl_pts.mgz
>*orig_nu.mgz  *

wm.asegedit.mgzaseg.auto_noCCseg.mgz   filled.mgz
>   rawavg.mgz wm.mgz

aseg.mgzlh.ribbon.mgz
>rh.ribbon.mgz wm.seg.mgz
>   aseg.presurf.hypos.mgz

ribbon.mgz   wmparc.mgz


Best,
ping

Greve, Douglas N.,Ph.D.  于2019年6月23日周日 下午9:35写道：

> It does 1-3. It also labels cerebellum which you could then use to perform
> #4
>
> On 6/23/2019 7:03 AM, ping cao wrote:
>
> External Email - Use Caution
> Dear expert，
>
> Thank you for reading!
>
> I want to do these four pre-processing steps:
>
> 1. Re-sampling each MR image to 256*256*256;
> 2. Using the N3 algorithm for intensity inhomogeneity correction;
>
> 3. Skull stripping;
>
> 4. Removing the cerebellum.
>
> Does " *recon-all"*  do all the above 4 steps automatically? If so, which
> file is just finished with these four steps? If not, how can I do these
> steps?
>
> Your help is greatly appreciated.
>
>
> Best,
> ping
>
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Re: [Freesurfer] question for preprocessing

2019-06-23 Thread Greve, Douglas N.,Ph.D.

It does 1-3. It also labels cerebellum which you could then use to perform #4

On 6/23/2019 7:03 AM, ping cao wrote:

External Email - Use Caution

Dear expert，

Thank you for reading!

I want to do these four pre-processing steps:
1. Re-sampling each MR image to 256*256*256;
2. Using the N3 algorithm for intensity inhomogeneity correction;
3. Skull stripping;
4. Removing the cerebellum.
Does " recon-all"  do all the above 4 steps automatically? If so, which file is 
just finished with these four steps? If not, how can I do these steps?

Your help is greatly appreciated.

Best,
ping



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[Freesurfer] I have a question for "matlabruntime"

[Freesurfer] (no subject)

Re: [Freesurfer] voxel coordinates of corpus collosum

Re: [Freesurfer] question for preprocessing

Re: [Freesurfer] question for preprocessing

Re: [Freesurfer] question for preprocessing

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