Re: [Freesurfer] Question regarding Volumetric masks

[Douglas N Greve]

Hi Antonella, if you are using something from FSL, you should be posting 
to the FSL list. As I said before, I don't know where the JHU atlas came 
from or what space it is in. It does not appear that this application is 
related to the FreeSurfer tools. I bet the FSL folks could answer your 
question much more quickly and accurately than I can.
doug


On 07/27/2012 01:12 PM, Antonella Kis wrote:
> Hi Doug,
>
> Thanks again for your prompt reply.
>
> I have from FSL a JHU-WhiteMatter-labels-1mm.nii.gz file and for the 
> segmentations labels I have the JHU-WhiteMatter-labels-1mm.txt as you 
> can see in the attached files.
>
> Are them OK to be used?
>
> When you say to align my low b image to JHU atlas you mean to use Flirt ?
>
> Many thank.
> Antonella
> 
> *From:* Douglas N Greve 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Friday, July 27, 2012 12:10 PM
> *Subject:* Re: [Freesurfer] Question regarding Volumetric masks
>
> I don't know anything about the JHU atlas. If you have an anatomical in
> line with the JHU atlas, then align your low b image directly to that.
> You can then map the JHU atlas into the native diffusion space with
> mri_label2vol.
> doug
>
> On 07/27/2012 12:08 PM, Antonella Kis wrote:
> > Hi Doug,
> >
> > Sorry to bother with the same issue, I just remembered something. My
> > DTI data for each individual subjects is registered on the MNI152
> > using Flirt so I wonder if I should first register the atlas to the
> > MNI and then apply to my subjects. Can I do this? Then do I need to
> > run the mri_convert?
> >
> > Thanks again for your help.
> > Antonella
> >
> > 
> > *From:* Douglas N Greve  >
> > *To:* freesurfer@nmr.mgh.harvard.edu 
> 
> > *Sent:* Friday, July 27, 2012 11:09 AM
> > *Subject:* Re: [Freesurfer] Question regarding Volumetric masks
> >
> > Steps 2 and 3 look ok. The first step will probably fail. You need a
> > registration between the JHU atlas and the individual. The people who
> > developed the JHU atlas can probably tell you how to do this.
> > doug
> >
> > On 07/27/2012 10:39 AM, Antonella Kis wrote:
> > >
> > >
> > >
> > > Dear All,
> > >
> > > I want to use cingulate bundle as ROIs more exactly mask for fiber
> > > tracking.
> > > Can someone explain please how I can use the
> > > JHU-WhiteMatter-labels-1mm.nii.gz and their labels
> > > JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingulate bundle in
> > > my diffusion space for each individual subjects?
> > > Do I need to draw ROIs and how I can do this more accurate?
> > >
> > > Is the following correct:
> > >
> > > 1) /mri_convert -rl [path to subject]/DATA/s001/nodif.nii.gz -rt
> > > nearest /JHU-WhiteMatter-labels-1mm.nii.gz /s001_aseg2dif.nii.gz/
> > >
> > > /2) /fslmaths //[path to subject]/DATA//s001_aseg2dif.nii.gz -uthr 35
> > > -thr 35 /[path to working
> > > directory]/ROIS/Cingulum_(cingulate_gyrus)_R.nii.gz
> > >
> > > 3) fslmaths Cingulum_(cingulate_gyrus)_R.nii.gz –div 35
> > > Cingulum_(cingulate_gyrus)_R.nii.gz
> > >
> > >
> > > If I want to run for the cingulate bundle the tractography should I
> > > repeat this steps for:
> > >
> > >
> > > 36 Cingulum_(cingulate_gyrus)_L
> > > 37 Cingulum_(hippocampus)_R
> > > 38 Cingulum_(hippocampus)_L
> > >
> > >
> > >
> > >
> > > Thank you for your help.
> > > Antonella
> > >
> > >
> > >
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu 
>  
>  >
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu  
> >
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
> > 
> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
> > 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu 
>  
>  >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to whom
> > it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains pa

[Freesurfer] pial edit question

[Cat Chong]

Dear Experts,

I am occasionally noticing some 'pinching' on the inflated brain surfaces 
around the temporal lobe pole. When I check the brainmask.mgz files, the raised 
areas are due to a 'bubble' of pial surface forming on top of pial surface. 
Upon checking white matter and grey matter boundaries, the pial surface should 
really not be separated as a "bubble", but should in fact be all one surface. 
What would you suggest would be the best way to fix this? The white matter 
seems to be fine.
Best Regards,
Catherine
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Re: [Freesurfer] Issues with Tracula

[Anastasia Yendiki]

The monitoring script that bedpostx runs and tells you if things have or 
haven't finished properly can't always be trusted. So if that's the only 
error message you see, I wouldn't worry about it. Have the *ph1* and *th1* 
files appeared this time?


On Fri, 27 Jul 2012, Sergio Medina wrote:


What a coincide! Our teams have both chosen the same release cycle strategy
:P

I ran bedpostx_postproc and I've got so many errors that makes me think the
problem is before this step (see output in attached
n1-bedpostx-postproc.txt).

So, I ran again bedpostx on the dmri directory, which the first run *seemed*
to finish and didn't throw any error (I attached the output in the first
email).
This run did finish, and it did throw errors (full output in
n2-bedpostx-dmri.txt):

[...]
slice 63 has already been processed
wc: /volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt: No such
file or directory
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
results carefully.
kill: 276: No such process

Then I started wondering whether I do have the right data to actually run
bedpostx, so I run the script that checks that: bedpostx_datacheck, the
output (n3-bedpostx-datacheck.txt) doesn't show any signs of errors so I
would like to assume everything is ok with the input data...

Any idea?

Thanks, once again.

Sergio.


2012/7/27 Anastasia Yendiki 

  Hi Sergio - As with any imminent new version release, it's
  happening "soon". I'd say in a month, I'm just not sure a month
  from when :P

  The fact that the temporary files (everything with *slice* in
  the name) are still in your bedpostx directory means that
  bedpostx didn't finish running properly. You can try running the
  last step of bedpostx and see if you get any error messages that
  give you any clues:
          bedpostx_postproc.sh
  /volatile/tracula/results/Diff001/dmri

  Normally this step merges the individual slices into volumes and
  deletes the temporary files. If all else fails, I'd ask the FSL
  gurus.

  Hope this helps,
  a.y

  On Fri, 27 Jul 2012, Sergio Medina wrote:

Anastasia,

Thanks for such a quick reply!

Please find my answers inline...

2012/7/26 Anastasia Yendiki


      Hi Sergio - Thank you for your kind words, and
also thank you
      for taking the time to search the archives for
answers!


      The first problems you had with running
bedpostx through
      trac-all have to do with trac-all assuming an
older version of
      FSL than the current one, and this'll be fixed
in the upcoming
      release of trac-all. Indeed the thing to do in
the meantime is
      to run bedpostx by itself, as you did. I
apologize for the
      inconvenience.


Great! By any chance, do you know when that release
will happen?
 

      About the problem you had when you ran
bedpostx directly: do you
      get the other outputs of bedpostx, listed
here? Are there any
      other, temporary files left over as well?
             
http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html



I have all of them, except for nodif_brain. And I
only have the ones with
i=2 while I should have the ones with i=1 too.
Attached you can find two files, the output of ls
-Rah on both dmri and
dmri.bedpostX directories.

 


      The merged_ph?samples are the orientation
angles of the each of
      the two anisotropic compartments ("sticks",
"fibers", whatever
      you want to call them) that bedpostx fit in
each voxel. So "1"
      is the orientation angle of the largest
stick/fiber, and "2" the
      one of the 2nd largest. If there's a "2",
there should be a "1"!


But there are not :(
 

      Also, I looked at your dmrirc file and noticed
that you
      decreased the # of control points b/c you hate
waiting :) I just
      wanted to warn you that decreasing that #
might make you wait
      longer b/c make fitting a spline with fewer
control points to
      initialize the algorithm is sometimes more
challenging.


Hehe, thanks! I changed it back to 5 now...
 
Thanks!

Sergio.


      Hope this helps,
      a.y

      On Thu

Re: [Freesurfer] Question regarding Volumetric masks

[Douglas N Greve]

I don't know anything about the JHU atlas. If you have an anatomical in 
line with the JHU atlas, then align your low b image directly to that. 
You can then map the JHU atlas into the native diffusion space with 
mri_label2vol.
doug

On 07/27/2012 12:08 PM, Antonella Kis wrote:
> Hi Doug,
>
> Sorry to bother with the same issue, I just remembered something. My 
> DTI data for each individual subjects is registered on the MNI152 
> using Flirt so I wonder if I should first register the atlas to the 
> MNI and then apply to my subjects. Can I do this? Then do I need to 
> run the mri_convert?
>
> Thanks again for your help.
> Antonella
>
> 
> *From:* Douglas N Greve 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Friday, July 27, 2012 11:09 AM
> *Subject:* Re: [Freesurfer] Question regarding Volumetric masks
>
> Steps 2 and 3 look ok. The first step will probably fail. You need a
> registration between the JHU atlas and the individual. The people who
> developed the JHU atlas can probably tell you how to do this.
> doug
>
> On 07/27/2012 10:39 AM, Antonella Kis wrote:
> >
> >
> >
> > Dear All,
> >
> > I want to use cingulate bundle as ROIs more exactly mask for fiber
> > tracking.
> > Can someone explain please how I can use the
> > JHU-WhiteMatter-labels-1mm.nii.gz and their labels
> > JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingulate bundle in
> > my diffusion space for each individual subjects?
> > Do I need to draw ROIs and how I can do this more accurate?
> >
> > Is the following correct:
> >
> > 1) /mri_convert -rl [path to subject]/DATA/s001/nodif.nii.gz -rt
> > nearest /JHU-WhiteMatter-labels-1mm.nii.gz /s001_aseg2dif.nii.gz/
> >
> > /2) /fslmaths //[path to subject]/DATA//s001_aseg2dif.nii.gz -uthr 35
> > -thr 35 /[path to working
> > directory]/ROIS/Cingulum_(cingulate_gyrus)_R.nii.gz
> >
> > 3) fslmaths Cingulum_(cingulate_gyrus)_R.nii.gz –div 35
> > Cingulum_(cingulate_gyrus)_R.nii.gz
> >
> >
> > If I want to run for the cingulate bundle the tractography should I
> > repeat this steps for:
> >
> >
> > 36 Cingulum_(cingulate_gyrus)_L
> > 37 Cingulum_(hippocampus)_R
> > 38 Cingulum_(hippocampus)_L
> >
> >
> >
> >
> > Thank you for your help.
> > Antonella
> >
> >
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom 
> it is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you 
> in error
> but does not contain patient information, please contact the sender 
> and properly
> dispose of the e-mail.
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] problem when convert dcm to mgz

[Douglas N Greve]

Can you send the result of
mri_probedicom --i 
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm


doug


On 07/27/2012 05:38 AM, Liu Yawu wrote:
> Hi,
> I recently install Freesurfer under ubuntu. I tested two own data. It works 
> in one our own case, but did not work for other cases. The problem is the 
> Freesurfer "not found or unknown file type for file 
> /home/d4201z/Desktop/im_4/2000110815073505086.dcm" when convert convert 
> dcm to mgz. Any helps are appreciated!
>
> Here are detailed inf:
>
>
> FREESURFER_HOME: /usr/local/src/freesurfer
>
> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>
> Debian version: wheezy/sid
>
> Kernel info: Linux 3.2.0-27-generic x86_64
>
>
> 1. the entire command-line executed
> recon-all -s APauli \
> -i 
> /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm
>
> 2. the error message generated
>
> file not found or unknown file type for file 
> /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm
>
>
> 3. the subject's /script/recon-all.log
>
> Fri Jul 27 12:20:31 EEST 2012
> /usr/local/src/freesurfer/subjects/APauli
> /usr/local/src/freesurfer/bin/recon-all
> -s APauli -i 
> /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm
> subjid APauli
> setenv SUBJECTS_DIR /usr/local/src/freesurfer/subjects
> FREESURFER_HOME /usr/local/src/freesurfer
> Actual FREESURFER_HOME /usr/local/src/freesurfer
> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
> Linux d4201z-CELSIUS-M470-2 3.2.0-27-generic #43-Ubuntu SMP Fri Jul 6 
> 14:25:57 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
> cputime  unlimited
> filesize unlimited
> datasize unlimited
> stacksize8192 kbytes
> coredumpsize 0 kbytes
> memoryuseunlimited
> vmemoryuse   unlimited
> descriptors  1024
> memorylocked 64 kbytes
> maxproc  95900
> maxlocks unlimited
> maxsignal95900
> maxmessage   819200
> maxnice  0
> maxrtprio0
> maxrttimeunlimited
>
>   total   used   free sharedbuffers cached
> Mem:  1229825228804849417768  0 127152 973356
> -/+ buffers/cache:1779976   10518276
> Swap: 19529724  0   19529724
>
> 
> program versions used
> $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
> $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
> mri_convert -all-info
> ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: 
> stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 2011 
> 08:23:31  CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ 
>  User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
> PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
> FLIRT version 5.5
> $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
> mri_convert --version
> stable5
> ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
> $Name: stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 
> 2011 08:23:31  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve 
> Exp $  User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
> PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
> Program nu_correct, built from:
> Package MNI N3, version 1.10, compiled by nicks@minerva 
> (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
> ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 
> 2011 08:23:31  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp 
> $  User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
> PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
> ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 
> 2011 08:23:31  CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl 
> Exp $  User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
> PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
> ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 
> 2011 08:23:31  CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks 
> Exp $  User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
> PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
> ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
> stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 2011 
> 08:23:31  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  
> User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform

Re: [Freesurfer] Question regarding Volumetric masks

[Antonella Kis]

Hi Doug,

Sorry to bother with the same issue, I just remembered something. My DTI data 
for each individual subjects is registered on the MNI152 using Flirt so I 
wonder if I should first register the atlas to the MNI and then apply to my 
subjects. Can I do this? Then do I need to run the mri_convert?

Thanks again for your help.
Antonella




 From: Douglas N Greve 
To: freesurfer@nmr.mgh.harvard.edu 
Sent: Friday, July 27, 2012 11:09 AM
Subject: Re: [Freesurfer] Question regarding  Volumetric masks
 
Steps 2 and 3 look ok. The first step will probably fail. You need a 
registration between the JHU atlas and the individual. The people who 
developed the JHU atlas can probably tell you how to do this.
doug

On 07/27/2012 10:39 AM, Antonella Kis wrote:
>
>
>
> Dear All,
>
> I want to use cingulate bundle as ROIs more exactly mask for fiber 
> tracking.
> Can someone explain please how I can use the 
> JHU-WhiteMatter-labels-1mm.nii.gz and their labels 
> JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingulate bundle in 
> my diffusion space for each individual subjects?
> Do I need to draw ROIs and how I can do this more accurate?
>
> Is the following correct:
>
> 1) /mri_convert -rl [path to subject]/DATA/s001/nodif.nii.gz -rt 
> nearest /JHU-WhiteMatter-labels-1mm.nii.gz /s001_aseg2dif.nii.gz/
>
> /2) /fslmaths //[path to subject]/DATA//s001_aseg2dif.nii.gz -uthr 35 
> -thr 35 /[path to working 
> directory]/ROIS/Cingulum_(cingulate_gyrus)_R.nii.gz
>
> 3) fslmaths Cingulum_(cingulate_gyrus)_R.nii.gz –div 35 
> Cingulum_(cingulate_gyrus)_R.nii.gz
>
>
> If I want to run for the cingulate bundle the tractography should I 
> repeat this steps for:
>
>
> 36 Cingulum_(cingulate_gyrus)_L
> 37 Cingulum_(hippocampus)_R
> 38 Cingulum_(hippocampus)_L
>
>
>
>
> Thank you for your help.
> Antonella
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
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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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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Issues with Tracula

[Sergio Medina]

What a coincide! Our teams have both chosen the same release cycle strategy
:P

I ran bedpostx_postproc and I've got so many errors that makes me think the
problem is before this step (see output in attached
n1-bedpostx-postproc.txt).

So, I ran again bedpostx on the dmri directory, which the first run
*seemed* to finish and didn't throw any error (I attached the output in the
first email).
This run did finish, and it did throw errors (full output in
n2-bedpostx-dmri.txt):

*[...]*
*slice 63 has already been processed
wc: /volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt: No such
file or directory
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
results carefully.
kill: 276: No such process*

Then I started wondering whether I do have the right data to actually run
bedpostx, so I run the script that checks that: bedpostx_datacheck, the
output (n3-bedpostx-datacheck.txt) doesn't show any signs of errors so I
would like to assume everything is ok with the input data...

Any idea?

Thanks, once again.

Sergio.


2012/7/27 Anastasia Yendiki 

>
> Hi Sergio - As with any imminent new version release, it's happening
> "soon". I'd say in a month, I'm just not sure a month from when :P
>
> The fact that the temporary files (everything with *slice* in the name)
> are still in your bedpostx directory means that bedpostx didn't finish
> running properly. You can try running the last step of bedpostx and see if
> you get any error messages that give you any clues:
> bedpostx_postproc.sh /volatile/tracula/results/**Diff001/dmri
>
> Normally this step merges the individual slices into volumes and deletes
> the temporary files. If all else fails, I'd ask the FSL gurus.
>
> Hope this helps,
> a.y
>
>
> On Fri, 27 Jul 2012, Sergio Medina wrote:
>
>  Anastasia,
>>
>> Thanks for such a quick reply!
>>
>> Please find my answers inline...
>>
>> 2012/7/26 Anastasia Yendiki 
>>
>>   Hi Sergio - Thank you for your kind words, and also thank you
>>   for taking the time to search the archives for answers!
>>
>>
>>   The first problems you had with running bedpostx through
>>   trac-all have to do with trac-all assuming an older version of
>>   FSL than the current one, and this'll be fixed in the upcoming
>>   release of trac-all. Indeed the thing to do in the meantime is
>>   to run bedpostx by itself, as you did. I apologize for the
>>   inconvenience.
>>
>>
>> Great! By any chance, do you know when that release will happen?
>>
>>
>>   About the problem you had when you ran bedpostx directly: do you
>>   get the other outputs of bedpostx, listed here? Are there any
>>   other, temporary files left over as well?
>>   
>> http://www.fmrib.ox.ac.uk/fsl/**fdt/fdt_bedpostx.html
>>
>>
>>
>> I have all of them, except for nodif_brain. And I only have the ones with
>> i=2 while I should have the ones with i=1 too.
>> Attached you can find two files, the output of ls -Rah on both dmri and
>> dmri.bedpostX directories.
>>
>>
>>
>>
>>   The merged_ph?samples are the orientation angles of the each of
>>   the two anisotropic compartments ("sticks", "fibers", whatever
>>   you want to call them) that bedpostx fit in each voxel. So "1"
>>   is the orientation angle of the largest stick/fiber, and "2" the
>>   one of the 2nd largest. If there's a "2", there should be a "1"!
>>
>>
>> But there are not :(
>>
>>
>>   Also, I looked at your dmrirc file and noticed that you
>>   decreased the # of control points b/c you hate waiting :) I just
>>   wanted to warn you that decreasing that # might make you wait
>>   longer b/c make fitting a spline with fewer control points to
>>   initialize the algorithm is sometimes more challenging.
>>
>>
>> Hehe, thanks! I changed it back to 5 now...
>>
>> Thanks!
>>
>> Sergio.
>>
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Thu, 26 Jul 2012, Sergio Medina wrote:
>>
>>   Hi!
>>
>>   First of all let me thank you for having put at our
>>   disposal such great
>>   tools as FreeSurfer and Tracula!
>>   I am trying to run Tracula on the sample data that is on
>>   the website, but
>>   I've been running into some issues.
>>   I am attaching the configuration file just in case
>>   (dmrirc_single_subject-serch).
>>
>>   The first step "trac-all -prep" seems to run fine.
>>   The first problem comes with the second step "trac-all
>>   -bedp". The complete
>>   trace is included in the attached file
>>   1-error-trac-all-bedp.txt
>> After finding this on the FreeSurfer mailinglisthttps://mail.nmr.**
>> mgh.harvard.edu/pipermail//**freesurfer/2012-May/024042
>> .
>> html
>> I changed the lines
>>
>> ${BPDIR}/fsl_su

Re: [Freesurfer] Question regarding Volumetric masks

[Douglas N Greve]

Steps 2 and 3 look ok. The first step will probably fail. You need a 
registration between the JHU atlas and the individual. The people who 
developed the JHU atlas can probably tell you how to do this.
doug

On 07/27/2012 10:39 AM, Antonella Kis wrote:
>
>
>
> Dear All,
>
> I want to use cingulate bundle as ROIs more exactly mask for fiber 
> tracking.
> Can someone explain please how I can use the 
> JHU-WhiteMatter-labels-1mm.nii.gz and their labels 
> JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingulate bundle in 
> my diffusion space for each individual subjects?
> Do I need to draw ROIs and how I can do this more accurate?
>
> Is the following correct:
>
> 1) /mri_convert -rl [path to subject]/DATA/s001/nodif.nii.gz -rt 
> nearest /JHU-WhiteMatter-labels-1mm.nii.gz /s001_aseg2dif.nii.gz/
>
> /2) /fslmaths //[path to subject]/DATA//s001_aseg2dif.nii.gz -uthr 35 
> -thr 35 /[path to working 
> directory]/ROIS/Cingulum_(cingulate_gyrus)_R.nii.gz
>
> 3) fslmaths Cingulum_(cingulate_gyrus)_R.nii.gz –div 35 
> Cingulum_(cingulate_gyrus)_R.nii.gz
>
>
> If I want to run for the cingulate bundle the tractography should I 
> repeat this steps for:
>
>
> 36 Cingulum_(cingulate_gyrus)_L
> 37 Cingulum_(hippocampus)_R
> 38 Cingulum_(hippocampus)_L
>
>
>
>
> Thank you for your help.
> Antonella
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] WM/Pial surfs Problem with SPGRs from 3T GE

[Thomas Fink]

Hey experts,

Thank you very much for your advice!

So I guess my best guess would be to use recon-all with -nuintensitycor-3T
and add an expert option file for "-b 20" and "-n 5".
These flags belong to the "mri_normalize" binary?

Best regards
Thomas


On Thu, Jul 26, 2012 at 4:12 PM, Bruce Fischl wrote:

> Hi Michael
>
> that's a good thought. Let me talk to Nick, and see if we should default
> to it and have a 1.5T flag instead
>
> Bruce
>
> On Thu, 26 Jul 2012, Michael Waskom wrote:
>
>  Yes, that flag still works in 5.1.
>> Bruce, think these parameters could be default in 5.2?  It's a long extra
>> flag (that is, I imagine, someone arcane knowledge) for what has to be the
>> overwhelmingly modal field strength these days.
>>
>> Sorry to hijack, but this would be nice!
>>
>> Cheers,
>> Michael
>>
>> On Wed, Jul 25, 2012 at 10:29 PM, Mehul Sampat 
>> wrote:
>>   Hi Thomas,
>> The following message posted by Michael Harms
>> http://www.mail-archive.com/**freesur...@nmr.mgh.harvard.**
>> edu/msg20991.html
>> has some very useful options. I recently noticed that they help us
>> with a very similar problem...
>>
>> Also, I recall that for FS v5.0 there was a flag -nuintensitycor-3T
>> for "optimal parameters for nu_correct for 3T scans"
>> (as described in release notes for v5.0.)
>>
>> Bruce, the -nuintensitycor-3T is still available in v5.1 right?
>> If yes, then we could combine the options the two set of options and
>> run recon-all with "-b 20 -n 5 and  -nuintensitycor-3T"  for
>> the 3T scans? Would this be reasonable or does this combination not
>> recommended ?
>>
>> Thanks
>> Mehul
>>
>>
>>
>>
>>
>>
>> On Tue, Jul 24, 2012 at 12:47 AM, Thomas Fink
>>  wrote:
>>   Hey Experts,
>>
>>   As you can see from the picture, the autorecon does not
>>   work properly (for WM/Pial surfs) with my files:
>>   Especially in the temporal lobes.
>>
>>   I am working with the SPGR files of a 3T GE Machine.
>>   Is there any way to optimize the autorecon results for
>>   SPGRs?
>>   (Except the lavish application of CPs.)
>>
>>   Best regards
>>   Thomas
>>
>
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[Freesurfer] Question regarding Volumetric masks

[Antonella Kis]

Dear All,

I want  to use cingulate bundle as ROIs more exactly mask  for fiber tracking. 
Can someone explain please how I can use the JHU-WhiteMatter-labels-1mm.nii.gz 
and their labels JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingulate 
bundle in my diffusion space for each individual subjects?
Do I need to draw ROIs and how I can do this more accurate?


Is the following correct:

1) mri_convert -rl [path to subject]/DATA/s001/nodif.nii.gz  -rt  nearest  
JHU-WhiteMatter-labels-1mm.nii.gz  s001_aseg2dif.nii.gz

2) fslmaths /[path to subject]/DATA/s001_aseg2dif.nii.gz -uthr 35 -thr 35
/[path to working directory]/ROIS/Cingulum_(cingulate_gyrus)_R.nii.gz

3) fslmaths Cingulum_(cingulate_gyrus)_R.nii.gz –div 35 
Cingulum_(cingulate_gyrus)_R.nii.gz


If I want to run for the cingulate bundle the tractography should I repeat this 
steps for:


36    Cingulum_(cingulate_gyrus)_L 
37    Cingulum_(hippocampus)_R 
38    Cingulum_(hippocampus)_L




Thank you for your help.
Antonella___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Issues with Tracula

[Anastasia Yendiki]

Hi Sergio - As with any imminent new version release, it's happening 
"soon". I'd say in a month, I'm just not sure a month from when :P


The fact that the temporary files (everything with *slice* in the name) 
are still in your bedpostx directory means that bedpostx didn't finish 
running properly. You can try running the last step of bedpostx and see if 
you get any error messages that give you any clues:

bedpostx_postproc.sh /volatile/tracula/results/Diff001/dmri

Normally this step merges the individual slices into volumes and deletes 
the temporary files. If all else fails, I'd ask the FSL gurus.


Hope this helps,
a.y

On Fri, 27 Jul 2012, Sergio Medina wrote:


Anastasia,

Thanks for such a quick reply!

Please find my answers inline...

2012/7/26 Anastasia Yendiki 

  Hi Sergio - Thank you for your kind words, and also thank you
  for taking the time to search the archives for answers!


  The first problems you had with running bedpostx through
  trac-all have to do with trac-all assuming an older version of
  FSL than the current one, and this'll be fixed in the upcoming
  release of trac-all. Indeed the thing to do in the meantime is
  to run bedpostx by itself, as you did. I apologize for the
  inconvenience.


Great! By any chance, do you know when that release will happen?
 

  About the problem you had when you ran bedpostx directly: do you
  get the other outputs of bedpostx, listed here? Are there any
  other, temporary files left over as well?
          http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html



I have all of them, except for nodif_brain. And I only have the ones with
i=2 while I should have the ones with i=1 too.
Attached you can find two files, the output of ls -Rah on both dmri and
dmri.bedpostX directories.

 


  The merged_ph?samples are the orientation angles of the each of
  the two anisotropic compartments ("sticks", "fibers", whatever
  you want to call them) that bedpostx fit in each voxel. So "1"
  is the orientation angle of the largest stick/fiber, and "2" the
  one of the 2nd largest. If there's a "2", there should be a "1"!


But there are not :(
 

  Also, I looked at your dmrirc file and noticed that you
  decreased the # of control points b/c you hate waiting :) I just
  wanted to warn you that decreasing that # might make you wait
  longer b/c make fitting a spline with fewer control points to
  initialize the algorithm is sometimes more challenging.


Hehe, thanks! I changed it back to 5 now...
 
Thanks!

Sergio.


  Hope this helps,
  a.y

  On Thu, 26 Jul 2012, Sergio Medina wrote:

  Hi!

  First of all let me thank you for having put at our
  disposal such great
  tools as FreeSurfer and Tracula!
  I am trying to run Tracula on the sample data that is on
  the website, but
  I've been running into some issues.
  I am attaching the configuration file just in case
  (dmrirc_single_subject-serch).

  The first step "trac-all -prep" seems to run fine.
  The first problem comes with the second step "trac-all
  -bedp". The complete
  trace is included in the attached file
  1-error-trac-all-bedp.txt
After finding this on the FreeSurfer 
mailinglisthttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024042.
html
I changed the lines

${BPDIR}/fsl_sub_seychelles

for

${FSL_BIN}/fsl_sub

in the bedpostx_seychelles and I could continue, until the
script seems to
be stuck

Queuing parallel processing stage
/volatile/tracula/results/Diff001/dmri.bedpostX/monitor
0 slices processed
1 slices processed
1 slices processed
1 slices processed <== this line keeps on repeating

Following a suggestion I found on this other archived email
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html
I ran bedpostx on the dmri directory and seemed to succeed. I am
attaching
the output (2-bedpostx-dmri.txt).

Then I tried to run  trac-all -path but it stops with the
following error:

niiRead(): error opening file
/volatile/tracula/results/Diff001/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read
/volatile/tracula/results/Diff001/dmri.bedpostX/merged_ph1samples.nii.gz

I searched for that file everywhere but it doesn't exist. The
closest I
found was

results/Diff001/dmri.bedpostX/merged_ph2samples.nii.gz

Just in case I tried once again to run trac-all -bedp and this
time, after
having run bedpostx on the dmri directory, I get the following
error (the
whole output is in the attached 4-error-trac-all-bedp-2.txt
file):

[...]
slice 62 has already been processed
slice 63 has already been processed
wc:
/volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt: No
such
file or directory
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
results carefully.
kill: 390: No such proc

Re: [Freesurfer] problem when convert dcm to mgz

[Bruce Fischl]

Hi Yawu

where did you get that dicom from? Does the file you are pointing to 
exist?

cheers
Bruce

On Fri, 27 Jul 2012, Liu Yawu wrote:

> Hi,
> I recently install Freesurfer under ubuntu. I tested two own data. It works 
> in one our own case, but did not work for other cases. The problem is the 
> Freesurfer "not found or unknown file type for file 
> /home/d4201z/Desktop/im_4/2000110815073505086.dcm" when convert convert 
> dcm to mgz. Any helps are appreciated!
>
> Here are detailed inf:
>
>
> FREESURFER_HOME: /usr/local/src/freesurfer
>
> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>
> Debian version: wheezy/sid
>
> Kernel info: Linux 3.2.0-27-generic x86_64
>
>
> 1. the entire command-line executed
> recon-all -s APauli \
>   -i 
> /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm
>
> 2. the error message generated
>
> file not found or unknown file type for file 
> /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm
>
>
> 3. the subject's /script/recon-all.log
>
> Fri Jul 27 12:20:31 EEST 2012
> /usr/local/src/freesurfer/subjects/APauli
> /usr/local/src/freesurfer/bin/recon-all
> -s APauli -i 
> /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm
> subjid APauli
> setenv SUBJECTS_DIR /usr/local/src/freesurfer/subjects
> FREESURFER_HOME /usr/local/src/freesurfer
> Actual FREESURFER_HOME /usr/local/src/freesurfer
> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
> Linux d4201z-CELSIUS-M470-2 3.2.0-27-generic #43-Ubuntu SMP Fri Jul 6 
> 14:25:57 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
> cputime  unlimited
> filesize unlimited
> datasize unlimited
> stacksize8192 kbytes
> coredumpsize 0 kbytes
> memoryuseunlimited
> vmemoryuse   unlimited
> descriptors  1024
> memorylocked 64 kbytes
> maxproc  95900
> maxlocks unlimited
> maxsignal95900
> maxmessage   819200
> maxnice  0
> maxrtprio0
> maxrttimeunlimited
>
> total   used   free sharedbuffers cached
> Mem:  1229825228804849417768  0 127152 973356
> -/+ buffers/cache:1779976   10518276
> Swap: 19529724  0   19529724
>
> 
> program versions used
> $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
> $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
> mri_convert -all-info
> ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: 
> stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 2011 
> 08:23:31  CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ 
>  User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
> PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
> FLIRT version 5.5
> $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
> mri_convert --version
> stable5
> ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
> $Name: stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 
> 2011 08:23:31  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve 
> Exp $  User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
> PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
> Program nu_correct, built from:
> Package MNI N3, version 1.10, compiled by nicks@minerva 
> (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
> ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 
> 2011 08:23:31  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp 
> $  User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
> PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
> ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 
> 2011 08:23:31  CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl 
> Exp $  User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
> PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
> ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 
> 2011 08:23:31  CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks 
> Exp $  User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
> PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
> ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
> stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 2011 
> 08:23:31  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  
> User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
> PlatformVersion: 3.2.0-27-ge

Re: [Freesurfer] CSF and brain volume quantification.

[Bruce Fischl]

Hi Matthew

you could save the surfaces generated internally by mri_watershed with 
the -surf  option, compute the volume of the interior of that 
with mris_volume, then subtract out whatever other tissue classes you want 
using the aseg.

cheers
Bruce




On Fri, 27 Jul 2012, Matthew Goldfinger wrote:

> Dearest gurus of all things Freesurfer,
>  I am looking for a simple way to quantify the amount of CSF, the
> total volume of brain matter (excluding ventricular space if possible)
> and, as a check on these two, the total intracranial area. Essentially
> I need a way to compare how much room there is for the brain to move
> around and deform. Any ideas on how best to achieve these goals would
> be most appreciated.
>   Best,
>Matthew
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] FreeSurfer TrackVis Transforms

[Trietsch, Rayna]

Hi,

I would like to follow the workflow for the FreeSurfer TrackVis Transforms 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms) but I'm 
not sure how to get started. The first step is to load the trk data and divide 
the trk coordinates from the file by the voxel_size in the header. How do I do 
that? Is this done in matlab? Is there a way to export the trk coordinates into 
matlab? If anyone could help me get started with this, that would be great. 
Thanks.

~Rayna~

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Re: [Freesurfer] Issues with Tracula

[Sergio Medina]

Anastasia,

Thanks for such a quick reply!

Please find my answers inline...

2012/7/26 Anastasia Yendiki 

>
> Hi Sergio - Thank you for your kind words, and also thank you for taking
> the time to search the archives for answers!
>
>
> The first problems you had with running bedpostx through trac-all have to
> do with trac-all assuming an older version of FSL than the current one, and
> this'll be fixed in the upcoming release of trac-all. Indeed the thing to
> do in the meantime is to run bedpostx by itself, as you did. I apologize
> for the inconvenience.
>

Great! By any chance, do you know when that release will happen?


>
> About the problem you had when you ran bedpostx directly: do you get the
> other outputs of bedpostx, listed here? Are there any other, temporary
> files left over as well?
> 
> http://www.fmrib.ox.ac.uk/fsl/**fdt/fdt_bedpostx.html
>


I have all of them, except for nodif_brain. And I only have the ones with
i=2 while I should have the ones with i=1 too.
Attached you can find two files, the output of ls -Rah on both dmri and
dmri.bedpostX directories.



>
>
> The merged_ph?samples are the orientation angles of the each of the two
> anisotropic compartments ("sticks", "fibers", whatever you want to call
> them) that bedpostx fit in each voxel. So "1" is the orientation angle of
> the largest stick/fiber, and "2" the one of the 2nd largest. If there's a
> "2", there should be a "1"!
>

But there are not :(


>
> Also, I looked at your dmrirc file and noticed that you decreased the # of
> control points b/c you hate waiting :) I just wanted to warn you that
> decreasing that # might make you wait longer b/c make fitting a spline with
> fewer control points to initialize the algorithm is sometimes more
> challenging.
>

Hehe, thanks! I changed it back to 5 now...

Thanks!

Sergio.


> Hope this helps,
> a.y
>
> On Thu, 26 Jul 2012, Sergio Medina wrote:
>
>  Hi!
>>
>> First of all let me thank you for having put at our disposal such great
>> tools as FreeSurfer and Tracula!
>> I am trying to run Tracula on the sample data that is on the website, but
>> I've been running into some issues.
>> I am attaching the configuration file just in case
>> (dmrirc_single_subject-serch).
>>
>> The first step "trac-all -prep" seems to run fine.
>> The first problem comes with the second step "trac-all -bedp". The
>> complete
>> trace is included in the attached file 1-error-trac-all-bedp.txt
>> After finding this on the FreeSurfer mailing listhttps://mail.nmr.mgh.**
>> harvard.edu/pipermail//**freesurfer/2012-May/024042.**html
>>
>> I changed the lines
>>
>> ${BPDIR}/fsl_sub_seychelles
>>
>> for
>>
>> ${FSL_BIN}/fsl_sub
>>
>> in the bedpostx_seychelles and I could continue, until the script seems to
>> be stuck
>>
>> Queuing parallel processing stage
>> /volatile/tracula/results/**Diff001/dmri.bedpostX/monitor
>> 0 slices processed
>> 1 slices processed
>> 1 slices processed
>> 1 slices processed <== this line keeps on repeating
>>
>> Following a suggestion I found on this other archived email
>> http://www.mail-archive.com/**freesur...@nmr.mgh.harvard.**
>> edu/msg20815.html
>> I ran bedpostx on the dmri directory and seemed to succeed. I am attaching
>> the output (2-bedpostx-dmri.txt).
>>
>> Then I tried to run  trac-all -path but it stops with the following error:
>>
>> niiRead(): error opening file
>> /volatile/tracula/results/**Diff001/dmri.bedpostX/merged_**
>> ph1samples.nii.gz
>> ERROR: Could not read
>> /volatile/tracula/results/**Diff001/dmri.bedpostX/merged_**
>> ph1samples.nii.gz
>>
>> I searched for that file everywhere but it doesn't exist. The closest I
>> found was
>>
>> results/Diff001/dmri.bedpostX/**merged_ph2samples.nii.gz
>>
>> Just in case I tried once again to run trac-all -bedp and this time, after
>> having run bedpostx on the dmri directory, I get the following error (the
>> whole output is in the attached 4-error-trac-all-bedp-2.txt file):
>>
>> [...]
>> slice 62 has already been processed
>> slice 63 has already been processed
>> wc: /volatile/tracula/results/**Diff001/dmri.bedpostX/**commands.txt: No
>> such
>> file or directory
>> Queuing post processing stage
>> 64 slices processed
>> For some reason the bedpostX process DOES NOT appear
>> to have successfully completed. Please examine your
>> results carefully.
>> kill: 390: No such process
>>
>> I tried searching for a file named commands.txt but I couldn't find any.
>>
>> Here is the output of bugr:
>>
>> FREESURFER_HOME: /i2bm/local/freesurfer
>> Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0
>> Debian version: squeeze/sid
>> Kernel info: Linux 2.6.38-14-generic x86_64
>>
>> and the output of source $FREESURFER_HOME/**SetUpFreeSurfer.sh
>>
>>  freesurfer-Linux-centos4_x86_**64-st

[Freesurfer] problem when convert dcm to mgz

[Liu Yawu]

Hi,
I recently install Freesurfer under ubuntu. I tested two own data. It works in 
one our own case, but did not work for other cases. The problem is the 
Freesurfer "not found or unknown file type for file 
/home/d4201z/Desktop/im_4/2000110815073505086.dcm" when convert convert dcm 
to mgz. Any helps are appreciated!

Here are detailed inf:


FREESURFER_HOME: /usr/local/src/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

Debian version: wheezy/sid

Kernel info: Linux 3.2.0-27-generic x86_64


1. the entire command-line executed
recon-all -s APauli \
   -i 
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm

2. the error message generated

file not found or unknown file type for file 
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm


3. the subject's /script/recon-all.log

Fri Jul 27 12:20:31 EEST 2012
/usr/local/src/freesurfer/subjects/APauli
/usr/local/src/freesurfer/bin/recon-all
-s APauli -i 
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm
subjid APauli
setenv SUBJECTS_DIR /usr/local/src/freesurfer/subjects
FREESURFER_HOME /usr/local/src/freesurfer
Actual FREESURFER_HOME /usr/local/src/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux d4201z-CELSIUS-M470-2 3.2.0-27-generic #43-Ubuntu SMP Fri Jul 6 14:25:57 
UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 64 kbytes
maxproc  95900
maxlocks unlimited
maxsignal95900
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:  1229825228804849417768  0 127152 973356
-/+ buffers/cache:1779976   10518276
Swap: 19529724  0   19529724


program versions used
$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 2011 
08:23:31  CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $  
User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  PlatformVersion: 
3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 
2011 08:23:31  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve 
Exp $  User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva 
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 
2011 08:23:31  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  
PlatformVersion: 3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 2011 
08:23:31  CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $  
User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  PlatformVersion: 
3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 2011 
08:23:31  CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $  
User: d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  PlatformVersion: 
3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2012/07/27-09:20:31-GMT  BuildTimeStamp: May 22 2011 
08:23:31  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: 
d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Linux  PlatformVersion: 
3.2.0-27-generic  CompilerName: GCC  CompilerVersion: 30400
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2012/07/27-09:20:32-GMT  BuildTimeStamp: May 22 2011 
08:23:31  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: 
d4201z  Machine: d4201z-CELSIUS-M470-2  Platform: Lin