[Freesurfer] mri_convert Segmentation fault (core dumped) lubuntu 13.04

[Joerg Pfannmoeller]

Dear freesurfer administrators,

recently upgraded our system to freesurfer 5.2 on lubuntu 13.04. After the 
installation I accounted problems when testing freesurfer. tkmedit did not 
display the subject bert, instead an error message was shown:

tkmedit bert orig.mgz

===
ERROR: A segfault has occurred. This is not your fault,
  : but is most likely an unrecoverable error and has
  : made the program unstable.
  :
  : Please send the contents of the file .xdebug_tkmedit
  : that should be in this directory to freesurfer@nmr.mgh.harvard.edu
  :
  : Now exiting...
  :



Content of .xdebug_tkmedit is:

tkmedit started: Thu May  2 08:44:48 2013

/usr/local/freesurfer/tktools/tkmedit.bin bert orig.mgz 

$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $
Set user home dir to /home/mrt-physician/subjects
Set subject home dir to /home/mrt-physician/subjects/bert

Segfault
Importing volume with MRIread
xDebug stack (length: 5)
  04: Volm_ImportData( this=0x284adf70, 
isSource=/home/mrt-physician/subjects/bert/mri/orig.mgz )
  04: Importing volume with MRIread
03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 )
03: Reading data into volume
  02: ParseCmdLineArgs( argc=3, 
argv=/usr/local/freesurfer/tktools/tkmedit.bin )
  02: Loading volume orig.mgz
01: main()
01: Parsing command line arguments
  00: 
  00: 

As I found in the web this problem seems to be due to mri_convert on fedora 18 
(https://bugzilla.redhat.com/show_bug.cgi?id=905638). This bug is know 
reproduced for lubuntu 13.04. The output if mri_convert ist called is the 
following:

cd $SUBJECTS_DIR
mri_convert sample-001.mgz test.mgh 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from sample-001.mgz...
Segmentation fault (core dumped)

Is there a bugfix?

Sincerely yours

   Joerg
___
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.

Re: [Freesurfer] convert labels to volumetric masks

[Douglas Greve]

Hi Meng, I don't know anything about that atlas. What space is it in?
And how did you process the functional data?


On 5/1/13 9:14 PM, limengsecret wrote:
>
>
>   Hi Doug,
>
>
>   The relative freesurfer files were downloaded from
>   http://ltl.tkk.fi/wiki/Atlas about the retinotopic visual areas. And
>   I want to convert the files to volumetric masks to use for my own data.
>
>
>   The functional data have been preprocessed with slice-timing,
>   realignment, and normalization. And the masks overlay the functional
>   data created above to define the retinotopic visual areas.
>
>
>   Thank you!
>
> Meng
> *发件人：* Douglas N Greve 
> *发送时间：* 2013-05-02 02:02
> *收件人：* limengsecret 
> *抄送：* freesurfer 
> *主题：* Re: [Freesurfer] convert labels to volumetric masks
> Hi Meng,
> On 04/30/2013 09:53 PM, limengsecret wrote:
> > Hi Doug,
> > Thanks for your reply.
> > I have downloaded some freesurfer files (.annot, .label, .curv, .w)
> > about the specific regions.
> what do you mean you downloaded them? where did they come from exactly?
> Are they your own data?
> > And I want to convert this files to volumetric masks, then the masks
> > are used to overlay the normalized functional data, and according to
> > the mask to define the specific region as roi.
> How was your functional data normalized? Specifically what atlas was used?
> > Thus, the problem is that, how I can achieve this goal, and which
> > commands should I use.
> > Thanks a lot.
> > Best wishes,
> > Meng
> > Date: Mon, 29 Apr 2013 17:30:14 -0400
> > From: Douglas N Greve 
> > Subject: Re: [Freesurfer] convert labels to volumetric masks
> > To: freesurfer@nmr.mgh.harvard.edu
> > Message-ID: <517ee666.8050...@nmr.mgh.harvard.edu>
> > Content-Type: text/plain; charset=UTF-8; format=flowed
> > Hi Meng,
> > I don't understand what you are trying to do. Can you
> > elaborate? That command will simply check a registration that already
> > exists.
> > doug
> > On 04/29/2013 10:36 AM, limengsecret wrote:
> > Dear FreeSurfers,
> > I want to convert cortical labels to volumetric masks, the mask
> > created are used to register with the normalized functional data and
> > to define the roi, so could I run the following command?
> > tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg
> > ./register.dat/
> > and the func.nii has been normalized (sub.nii) to the MNI space. And
> > if the command is wrong, which command should I use?
> > Best wishes,
> > Meng
> >
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 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


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.

Re: [Freesurfer] convert labels to volumetric masks

[limengsecret]

Hi Doug,
The relative freesurfer files were downloaded from http://ltl.tkk.fi/wiki/Atlas 
about the retinotopic visual areas. And I want to convert the files to 
volumetric masks to use for my own data. 
The functional data have been preprocessed with slice-timing, realignment, and 
normalization. And the masks overlay the functional data created above to 
define the retinotopic visual areas. 
Thank you!
Meng

发件人： Douglas N Greve
发送时间： 2013-05-02 02:02
收件人： limengsecret
抄送： freesurfer
主题： Re: [Freesurfer] convert labels to volumetric masks
Hi Meng,

On 04/30/2013 09:53 PM, limengsecret wrote:
> Hi Doug,
> Thanks for your reply.
> I have downloaded some freesurfer files (.annot, .label, .curv, .w)
> about the specific regions.
what do you mean you downloaded them? where did they come from exactly?
Are they your own data?

> And I want to convert this files to volumetric masks, then the masks
> are used to overlay the normalized functional data, and according to
> the mask to define the specific region as roi.
How was your functional data normalized? Specifically what atlas was used?


> Thus, the problem is that, how I can achieve this goal, and which
> commands should I use.
> Thanks a lot.
> Best wishes,
> Meng
> Date: Mon, 29 Apr 2013 17:30:14 -0400
> From: Douglas N Greve 
> Subject: Re: [Freesurfer] convert labels to volumetric masks
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <517ee666.8050...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> Hi Meng,
> I don't understand what you are trying to do. Can you
> elaborate? That command will simply check a registration that already
> exists.
> doug
> On 04/29/2013 10:36 AM, limengsecret wrote:
> Dear FreeSurfers,
> I want to convert cortical labels to volumetric masks, the mask
> created are used to register with the normalized functional data and
> to define the roi, so could I run the following command?
> tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg
> ./register.dat/
> and the func.nii has been normalized (sub.nii) to the MNI space. And
> if the command is wrong, which command should I use?
> Best wishes,
> Meng
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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


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] Freesurfer License issue/bug on Opensuse 12.3

[Nick Jones]

Hi,

I've run into a license problem with the latest version of Freesurfer on 
OpenSuse 12.3. 64 bit.

FREESURFER_HOME: /usr/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
Kernel info: Linux 3.7.10-1.1-desktop x86_64

When running a test:

/usr/freesurfer>echo $shell
/bin/tcsh

/usr/freesurfer>source SetUpFreeSurfer.csh
 freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/freesurfer
FSFAST_HOME   /usr/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/freesurfer/subjects
MNI_DIR   /usr/freesurfer/mni
FSL_DIR   /usr/fsl

/usr/freesurfer>tkmedit bert orig.mgz
--
ERROR: Invalid FreeSurfer license key found in license file 
/usr/freesurfer/.license
   If you are outside the NMR-Martinos Center,
   go to http://surfer.nmr.mgh.harvard.edu to
   get a valid license file (it's free).
   If you are inside the NMR-Martinos Center,
   make sure to source the standard environment.
--

/usr/freesurfer>cat .license
hotm...@hotmail.com
14743
*C5.JPynIz8mt
/usr/freesurfer>

This license file has been obfuscated.

/usr/freesurfer>ll -a .license
-rw-r--r-- 1 root root 46 Apr 29 09:38 .license

/usr/freesurfer>cat VERSION
freesurfer-x86_64-unknown-linux-gnu-stable5-20130226

/usr/freesurfer>zypper targetos
openSUSE-12.3-x86_64

/usr/freesurfer>uname -a
Linux adams 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 UTC 2013 
(82d3f21) x86_64 x86_64 x86_64 GNU/Linux

Name: tcl
Version: 8.5.12-3.1.3
Name: tk
Version: 8.5.12-3.1.1

Thanks to anyone who can provide some insight or workaround.  I'm also curious 
if anyone knows the reasoning behind using this type of license mechanism, as 
opposed to agreeing to a license prior to downloading, like FSL or 3DSlicer?

Nick
___
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.

Re: [Freesurfer] Using the muscle ROI in the FreeSurferColorLUT

[Bruce Fischl]

Hi Jeff

our standard segmentation doesn't include muscle. We did have some 
prototypes that labeled all cranial muscles but they are not much more than 
prototypes
Bruce


On Wed, 1 May 2013, 
jwa...@nmr.mgh.harvard.edu wrote:

> Hello Freesurfers,
>  I would like to use the muscle ROI in the LUT (number 123).  Can anyone
> tell me which muscles (all cranial? cervical too?) are included?  I
> tried making a subject-specific label using the following command:
>  mri_cor2label --c
> /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aseg.mgz
> --id 123 --l
> /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/muscle_${identifier}.label
>
> This yielded the error "Found 0 label voxels", presumably because aseg.mgz
> is skull-stripped.  When I used orig.mgz instead of aseg.mgz in the
> command line above, the assigned label is a scattering of single voxels
> throughout the cortex and subcortical white matter.  I am guessing that
> this is because orig.mgz is not registered to the same space as aseg.mgz -
> is this correct?
>
> Any suggestions for how to use the muscle ROI would be much appreciated.
>
>  Thanks,
>   Jeff
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Using the muscle ROI in the FreeSurferColorLUT

[jwaugh]

Hello Freesurfers,
  I would like to use the muscle ROI in the LUT (number 123).  Can anyone
tell me which muscles (all cranial? cervical too?) are included?  I
tried making a subject-specific label using the following command:  
  mri_cor2label --c
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aseg.mgz
--id 123 --l
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/muscle_${identifier}.label

This yielded the error "Found 0 label voxels", presumably because aseg.mgz
is skull-stripped.  When I used orig.mgz instead of aseg.mgz in the
command line above, the assigned label is a scattering of single voxels
throughout the cortex and subcortical white matter.  I am guessing that
this is because orig.mgz is not registered to the same space as aseg.mgz -
is this correct?

Any suggestions for how to use the muscle ROI would be much appreciated.

  Thanks,
   Jeff
___
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.

Re: [Freesurfer] (no subject)

[Bruce Fischl]

Hi Ashley

yes, a bunch of times. The dura can cause some problems, but mostly they 
run ok

Bruce
On Wed, 1 May 2013, Ashley Hannah wrote:



Has anyone ever ran a post contrast sequence in FreeSurfer?

Thanks, 

Ashley
--


___
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] (no subject)

[Ashley Hannah]

Has anyone ever ran a post contrast sequence in FreeSurfer?
Thanks,

Ashley
-- 
*
*
___
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.

Re: [Freesurfer] convert labels to volumetric masks

[Douglas N Greve]

Hi Meng,

On 04/30/2013 09:53 PM, limengsecret wrote:
> Hi Doug,
> Thanks for your reply.
> I have downloaded some freesurfer files (.annot, .label, .curv, .w)
> about the specific regions.
what do you mean you downloaded them? where did they come from exactly?
Are they your own data?

> And I want to convert this files to volumetric masks, then the masks
> are used to overlay the normalized functional data, and according to
> the mask to define the specific region as roi.
How was your functional data normalized? Specifically what atlas was used?


> Thus, the problem is that, how I can achieve this goal, and which
> commands should I use.
> Thanks a lot.
> Best wishes,
> Meng
> Date: Mon, 29 Apr 2013 17:30:14 -0400
> From: Douglas N Greve 
> Subject: Re: [Freesurfer] convert labels to volumetric masks
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <517ee666.8050...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> Hi Meng,
> I don't understand what you are trying to do. Can you
> elaborate? That command will simply check a registration that already
> exists.
> doug
> On 04/29/2013 10:36 AM, limengsecret wrote:
> Dear FreeSurfers,
> I want to convert cortical labels to volumetric masks, the mask
> created are used to register with the normalized functional data and
> to define the roi, so could I run the following command?
> tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg
> ./register.dat/
> and the func.nii has been normalized (sub.nii) to the MNI space. And
> if the command is wrong, which command should I use?
> Best wishes,
> Meng
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] error in longitudinal processing "dimension mismatch"

[Bruce Fischl]

Keith


On Wed, May 1, 2013 at 12:43 PM, Bruce Fischl 
wrote:
  Hi Keith

  can you cc the list so that others can answer? Like Martin!

  thanks
  Bruce
  On Wed, 1 May 2013, Qi Wu wrote:

  Hi Bruce,
  Thank you so much for your quick reply.

  I used the following script to do the first step
  cross-sectional
  preprossessing

  #!/bin/tcsh -ef
  # add 'x' to '-ef' to trace code as it is executed

  # GO_FS1 - The "Easy" button #
  # Usage: GO_FS-123 
  # Feeds multiple subjects into autorecon1, autorecon2,
  and autorecon3
  # Requires that original scan data be placed in
  $SUBJECTS_DIR/_orig_
  # (Place each subject's anat series in separate
  folders)


  echo "\n <><><><><><><><><><><>< GO FreeSurfer!
  ><><><><><><><><><><><> \n"

  ### Check if subjects directory specified ###
  if ( "$1" != "" ) then
    set subjdir = $1
  else
    echo "\n ERROR: No subjects directory specified \n"
    exit 1
  endif

  ### Set FREESURFER_HOME and SUBJECTS_DIR ###

  setenv FREESURFER_HOME /usr/local/freesurfer5.1

  if ( -e
  /data/keith/freesurferdata/subjects_longitudinal/$subjdir)
  then
    setenv SUBJECTS_DIR
  /data/keith/freesurferdata/subjects_longitudinal/$subjdir
  else
    echo "\n ERROR: Specified subjects directory does not
  exist \n"
    exit 1
  endif

  ### Check if original scan data exists ###

  if ( ! -e /$SUBJECTS_DIR/_orig_ ) then
    echo "\n ERROR: Original scan data not found. \n"
    exit 1
  endif

  ### disable functional tools ###

  setenv NO_FSFAST

  # (To enable functional tools, disable the above line,
  enable the
  following:)
  # (HAVE NOT TESTED THIS YET) (MAYBE BETTER IF
  NO_FSFAST ANYWAYS)
  #setenv FUNCTIONALS_DIR $FREESURFER_HOME/sessions
  # echo "FUNCTIONALS_DIR = $FUNCTIONALS_DIR"
  # (and add the following to ~/matlab/startup.m)
  #fsfasthome = getenv('FSFAST_HOME');
  #fsfasttoolbox = sprintf('%s/toolbox',fsfasthome');
  #path(path,fsfasttoolbox);

  ### Set up FreeSurfer ###

  setenv prompt
  source $FREESURFER_HOME/FreeSurferEnv.csh
  echo ""


  ### List out directories in _orig_ , set subj array,
  prompt to continue ###

  echo "Found the following subjects: \n"

  set i = 0
  set subjID

  foreach d ($SUBJECTS_DIR/_orig_/*)
    @ i++
    set subjID = ($subjID $d:t)
    echo "   Subject "$i": " $subjID[$i]
  end
  set subjCount = $i

  set response
  while ($response != "n" && $response != "y")
    echo -n "\n Process these $subjCount subjects? [y/n] > "
    set response = $<
  end
  if ($response == "n") then
    echo "\n Program ended by user \n"
    exit 1
  endif


  ### Prompt user for First Anat Filename's ### 

  set firstAnatSame
  while ($firstAnatSame != "y" && $firstAnatSame != "n")
    echo -n "\n Are all the anat series named identically?
  [y/n]: > "
    set firstAnatSame = $<
  end
  switch ($firstAnatSame)
    case [y]:
      echo -n "\n Please enter the first filename (e.g.
  p1_000.dcm) for all
  anat series: > "
      set firstAnat = $<
      breaksw
    case [n]:
      echo "\n Please enter the first filename (e.g.
  p1_000.dcm) in the anat
  series for:"
      set i = 0
      set firstAnat
      while ($i < $subjCount)
        @ i++
        echo -n "    "$subjID[$i]": > "
        set firstAnat = ($firstAnat $<)
      end
      breaksw
  endsw


  ### Run autorecon1 for each subject ###

  cd $SUBJECTS_DIR

  switch ($firstAnatSame)
    case [y]:
      set i = 0
      while ($i < $subjCount)
        @ i++
      echo "\n<><><><><><><><><><><><| NOW PROCESSING
  <"$subjID[$i]">
  |><><><><><><><><><><><>\n"
        recon-all -i
  $SUBJECTS_DIR/_orig_/$subjID[$i]/$firstAnat -all -s
  $subjID[$i]
      end
      breaksw
    case [n]:
      set i = 0
      while ($i < $subjCount)
        @ i++
      echo "\n<><><><><><><><><><><><| NOW PROCESSING
  <"$subjID[$i]">
  |><><><><><><><><><><><>\n"
        recon-all -i
  $SUBJECTS_DIR/_orig_/$subjID[$i]/$firstAnat[$i] -all -s
  $subjID[$i]
      end
      breaksw
  endsw


  echo ""
  date +"Finished $0 without error at %T on %a %b %d %Y"
  echo ""
  exit 0

  ###
  ### Simple working loop
  #set i = 0
  #while ($i < 10)
  # echo $i
  # @ i++
  #end
  ###

  #
  ### TO DO ###
  #
  # why don't env's remain 'set' after running this? (they
  do after running
  SetUpFreeSurfer.csh or FreeSur

Re: [Freesurfer] incomplete tracts

[Anastasia Yendiki]

Hi Stefano - You'll have to include the log file, so that we can see the 
exact command line that was being run when the error happened.


Thanks,
a.y

On Wed, 1 May 2013, std...@virgilio.it wrote:


Hi Bruce,

trac-all -prep -c $FREESURFER_HOME/dmrirc_single_subject_d11_NEW.I'm also 
attaching dmrirc files.

Thank you very much.


Stefano



Messaggio originale
Da: fis...@nmr.mgh.harvard.edu
Data: 1-mag-2013 15.39
A: 
Cc: , 
Ogg: Re: [Freesurfer] R: Re:  R: Re:  R: Re:  R: Re:  incomplete tracts

Hi Stefano

you need to tell us what command you were running.

cheers
Bruce

On Wed, 1 May 2013,
std...@virgilio.it wrote:

>
> I have this error:
>
> writing registered surface
to/Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_av
> g35.sphere.reg...
> expanding nbhd size to 1
> 1109: 1 negative triangles
> mris_resample: Command not found.
>
> Thanks,
>
> Stefano
>
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 30-apr-2013 21.12
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re:  R: Re:  R: Re:  incomplete tracts
>
>
> Like I said in my previous email to you, please do not specify the CVS
> template. This means delete the cvstempdir line from your configuration
> file, or comment it out.
>
> On Tue, 30 Apr 2013, std...@virgilio.it wrote:
>
> > Hi Anastasia,
> > when I run the configuration file (which I'm attaching)
> > ERROR: Could not find CVS template
> >
> > I apologize but which is the correct directory of CVS template?
> >
> > Thanks,
> >
> >
> > Stefano
> >
> >
> > Messaggio originale
> > Da: ayend...@nmr.mgh.harvard.edu
> > Data: 26-apr-2013 20.08
> > A: 
> > Cc: 
> > Ogg: Re: [Freesurfer] R: Re:  R: Re:  incomplete tracts
> >
> >
> > Hi Stefano - Just use the default for that, you don't need to specify the
> > location.
> >
> > a.y
> >
> > On Sun, 21 Apr 2013, std...@virgilio.it wrote:
> >
> > > Hi Anastasia, 
> > > I apologize but I do not find CVS template? Where it should be located?
> > >
> > > Thank you very much,
> > >
> > >
> > > Stefano
> > >
> > >
> > >
> > > Messaggio originale
> > > Da: ayend...@nmr.mgh.harvard.edu
> > > Data: 9-apr-2013 17.50
> > > A: 
> > > Cc: 
> > > Ogg: Re: [Freesurfer] R: Re:  incomplete tracts
> > >
> > >
> > > Hi Stefano - Did you try CVS for the inter-subject registration? It
> > > doesn't look like it from the configuration file.
> > >
> > > a.y
> > >
> > > On Tue, 9 Apr 2013, std...@virgilio.it wrote:
> > >
> > > > Hi Anastasia,
> > > > yes, I tried.I'm attacking the last configuration file that I used.
> > > >
> > > > Thanks, 
> > > >
> > > >
> > > > Stefano
> > > >
> > > > Messaggio originale
> > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > Data: 9-apr-2013 1.42
> > > > A: 
> > > > Cc: 
> > > > Ogg: Re: [Freesurfer] incomplete tracts
> > > >
> > > >
> > > > What registration methods are you using for the intra-subject and
> > > > inter-subject registration? Have you tried the different options?
> > > >
> > > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > > >
> > > > > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely
> fminor.
> > > > >
> > > > > Messaggio originale
> > > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > > Data: 5-apr-2013 18.57
> > > > > A: 
> > > > > Cc: "freesurfer@nmr.mgh.harvard.edu"
> > > > > Ogg: Re: [Freesurfer] R: Re: R: Re:  incomplete tracts
> > > > >
> > > > >
> > > > > What you say "again" you mean with 5.2?
> > > > >
> > > > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > > > >
> > > > > > Hi Anastasia,
> > > > > > yes, for some subject the low-b volume is in the end.
> > > > > > Some subjects have again incomplete tracts.
> > > > > > I'm attacking an example of configuration file that I'm using.
> > > > > > I hope that you can check it please.
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > >
> > > > > > Stefano
> > > > > >
> > > > > > Messaggio originale
> > > > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > > > Data: 5-apr-2013 18.45
> > > > > > A: 
> > > > > > Cc:
> "freesurfer@nmr.mgh.harvard.edu"
> > > > > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts
> > > > > >
> > > > > >
> > > > > > Hi Stefano - In your case we determined that the ones that had the
> low-b
> > > > > > volume in the end didn't run correctly, right? In that case, I
> didn't
> > > > need
> > > > > > to see anything, you were going to try running 5.2.
> > > > > >
> > > > > > a.y
> > > > > >
> > > > > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > > > > >
> > > > > > > Hi Anastasia,
> > > > > > > could I send you the data of a subject that I don't run
> correctly? 
> > > > > > >
> > > > > > > I still have some subjects with tracts incomplete and I do not
> know if
> > > > > it depends
> > > > > > from
> > > > > > > my analysis or whether the images are not good.
> > > > > > >
> > > > > > > Thanks,
> > > > > > >
> > > > > > >
> > > > > > > Stefano
> > > > > > >
> > > > > > >
> > > > > > > Messaggio originale
> > > > > > > Da: ayend..

Re: [Freesurfer] error in longitudinal processing "dimension mismatch"

[Bruce Fischl]

Hi Keith

what were the recon-all command lines you ran?
Bruce
On Wed, 1 May 2013, Qi Wu 
wrote:



Dear Freesurfer experts,

I have a dataset of 2 time points. I ran into problems when I tried to use
the two-stage approach to pull out statistics such as the rate of change in
Freesurfer 5.1.

I could not even get the first stage working. The error messages I got were
“ERROR: MRISar1: Surf/Src dimension mismatch” “ERROR -11 : mri_glmfit did
not work?”

I did further trouble-shooting for this particular message "nv1 = 140942,
nv1 = 143525", and I found out that "143525" was in the "base" folder
(kp5_base), and "140942" was for the two longitudinally registered images
(kp5.long.kp5_base, and kp5b.long.kp5_base).

The command line I used was : “long_mris_slopes --qdec
./qdec/AS_long_qdec.dat --meas thickness --hemi lh --do-avg --do-rate
--do-pc1 --do-spc --do-stack --do-label --time weeks –nosmooth”.

The first three lines in the qdec file:

“fsid fsid-base weeks age sex FSS avgPain

kp5 kp5_base 0 48 0 4.1 7

kp5b kp5_base 20 48 0 8.6 6”

This error was similar to what was in a previous 
post(https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024576.htm
l by joost janssen Jun 29, 2012). I tried to fix any similar problems, but
still wasn’t able to get it working.

What else could I have been doing wrong?

The on screen error output is provided as follows

Many thanks

Keith

Postdoctoral fellow
Toronto Western Hospital
Toronto, Ontario
Canada

***

Parsing the qdec table: ./qdec/AS_long_qdec.dat

Working in SUBJECTS_DIR:
/data/keith/freesurferdata/subjects_longitudinal_5.1_old

Subject-Template: kp5_base

INFO: 2 TPs in kp5_base , mean age: 10.0

===


SUBJECT kp5_base Intersecting Within-Subject Cortex Label

cp/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/
label/lh.cortex.label/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.
long.cortex.label

mris_label_calc 
intersect/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base
/label/lh.cortex.label/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.
long.cortex.label/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.
long.cortex.label

LabelWrite: saving 
to/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.
long.cortex.label

===


SUBJECT kp5_base Stackinbg Within-Subject Maps

mri_concat/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/
surf/lh.thickness/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base
/surf/lh.thickness 
--o/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.l
ong.thickness-stack.mgh

ninputs = 2

Checking inputs

nframestot = 2

Allocing output

Done allocing

nframes = 2

Writing 
to/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.l
ong.thickness-stack.mgh

===


SUBJECT kp5_base Running Within-Subject GLM

Writing ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat ...

mri_glmfit 
--y/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.l
ong.thickness-stack.mgh --X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat
--allow-zero-dof --no-contrasts-ok --surf kp5_base lh 
--label/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.
long.cortex.label --glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm

Reading source 
surface/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.w
hite

Number of vertices 143525

Number of faces 287046

Total area 91438.851562

AvgVtxArea 0.637094

AvgVtxDist 0.873064

StdVtxDist 0.245806

$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $

cwd /data/keith/freesurferdata/subjects_longitudinal_5.1_old

cmdline mri_glmfit 
--y/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.l
ong.thickness-stack.mgh --X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat
--allow-zero-dof --no-contrasts-ok --surf kp5_base lh 
--label/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.
long.cortex.label --glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm

sysname Linux

hostname davissvr1.uhnres.utoronto.ca

machine x86_64

user qwu

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.l
ong.thickness-stack.mgh

logyflag 0

X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat

usedti 0

labelmask/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.
long.cortex.label

maskinv 0

glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory ./tmp-kp5_base_lh_thickness_6PR2rH

[Freesurfer] incomplete tracts

[stdp82]

Hi Bruce,
trac-all -prep -c $FREESURFER_HOME/dmrirc_single_subject_d11_NEW.I'm also 
attaching dmrirc files.
Thank you very much.

Stefano




Messaggio originale
Da: fis...@nmr.mgh.harvard.edu
Data: 1-mag-2013 15.39
A: 
Cc: , 
Ogg: Re: [Freesurfer] R: Re:  R: Re:  R: Re:  R: Re:  incomplete tracts

Hi Stefano

you need to tell us what command you were running.

cheers
Bruce

On Wed, 1 May 2013, 
std...@virgilio.it wrote:

> 
> I have this error:
> 
> writing registered surface 
to/Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_av
> g35.sphere.reg...
> expanding nbhd size to 1
> 1109: 1 negative triangles
> mris_resample: Command not found.
> 
> Thanks,
> 
> Stefano
> 
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 30-apr-2013 21.12
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re:  R: Re:  R: Re:  incomplete tracts
> 
> 
> Like I said in my previous email to you, please do not specify the CVS
> template. This means delete the cvstempdir line from your configuration
> file, or comment it out.
> 
> On Tue, 30 Apr 2013, std...@virgilio.it wrote:
> 
> > Hi Anastasia,
> > when I run the configuration file (which I'm attaching)
> > ERROR: Could not find CVS template
> >
> > I apologize but which is the correct directory of CVS template?
> >
> > Thanks,
> >
> >
> > Stefano
> >
> >
> > Messaggio originale
> > Da: ayend...@nmr.mgh.harvard.edu
> > Data: 26-apr-2013 20.08
> > A: 
> > Cc: 
> > Ogg: Re: [Freesurfer] R: Re:  R: Re:  incomplete tracts
> >
> >
> > Hi Stefano - Just use the default for that, you don't need to specify the
> > location.
> >
> > a.y
> >
> > On Sun, 21 Apr 2013, std...@virgilio.it wrote:
> >
> > > Hi Anastasia, 
> > > I apologize but I do not find CVS template? Where it should be located?
> > >
> > > Thank you very much,
> > >
> > >
> > > Stefano
> > >
> > >
> > >
> > > Messaggio originale
> > > Da: ayend...@nmr.mgh.harvard.edu
> > > Data: 9-apr-2013 17.50
> > > A: 
> > > Cc: 
> > > Ogg: Re: [Freesurfer] R: Re:  incomplete tracts
> > >
> > >
> > > Hi Stefano - Did you try CVS for the inter-subject registration? It
> > > doesn't look like it from the configuration file.
> > >
> > > a.y
> > >
> > > On Tue, 9 Apr 2013, std...@virgilio.it wrote:
> > >
> > > > Hi Anastasia,
> > > > yes, I tried.I'm attacking the last configuration file that I used.
> > > >
> > > > Thanks, 
> > > >
> > > >
> > > > Stefano
> > > >
> > > > Messaggio originale
> > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > Data: 9-apr-2013 1.42
> > > > A: 
> > > > Cc: 
> > > > Ogg: Re: [Freesurfer] incomplete tracts
> > > >
> > > >
> > > > What registration methods are you using for the intra-subject and
> > > > inter-subject registration? Have you tried the different options?
> > > >
> > > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > > >
> > > > > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely
> fminor.
> > > > >
> > > > > Messaggio originale
> > > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > > Data: 5-apr-2013 18.57
> > > > > A: 
> > > > > Cc: "freesurfer@nmr.mgh.harvard.edu"
> > > > > Ogg: Re: [Freesurfer] R: Re: R: Re:  incomplete tracts
> > > > >
> > > > >
> > > > > What you say "again" you mean with 5.2?
> > > > >
> > > > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > > > >
> > > > > > Hi Anastasia,
> > > > > > yes, for some subject the low-b volume is in the end.
> > > > > > Some subjects have again incomplete tracts.
> > > > > > I'm attacking an example of configuration file that I'm using.
> > > > > > I hope that you can check it please.
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > >
> > > > > > Stefano
> > > > > >
> > > > > > Messaggio originale
> > > > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > > > Data: 5-apr-2013 18.45
> > > > > > A: 
> > > > > > Cc:
> "freesurfer@nmr.mgh.harvard.edu"
> > > > > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts
> > > > > >
> > > > > >
> > > > > > Hi Stefano - In your case we determined that the ones that had the
> low-b
> > > > > > volume in the end didn't run correctly, right? In that case, I
> didn't
> > > > need
> > > > > > to see anything, you were going to try running 5.2.
> > > > > >
> > > > > > a.y
> > > > > >
> > > > > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > > > > >
> > > > > > > Hi Anastasia,
> > > > > > > could I send you the data of a subject that I don't run
> correctly? 
> > > > > > >
> > > > > > > I still have some subjects with tracts incomplete and I do not
> know if
> > > > > it depends
> > > > > > from
> > > > > > > my analysis or whether the images are not good.
> > > > > > >
> > > > > > > Thanks,
> > > > > > >
> > > > > > >
> > > > > > > Stefano
> > > > > > >
> > > > > > >
> > > > > > > Messaggio originale
> > > > > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > > > > Data: 5-apr-2013 17.37
> > > > > > > A: "Gerit Pfuhl"
> > > > > > > Cc:
> "freesurfer@nmr.mgh.harvard.edu"
> > > > > > > Ogg: Re: [Freesurfer] incomplete tra

[Freesurfer] error in longitudinal processing "dimension mismatch"

[Qi Wu]

Dear Freesurfer experts,

I have a dataset of 2 time points. I ran into problems when I tried to use
the two-stage approach to pull out statistics such as the rate of change in
Freesurfer 5.1.

I could not even get the first stage working. The error messages I got were
“ERROR: MRISar1: Surf/Src dimension mismatch” “ERROR -11 : mri_glmfit did
not work?”

I did further trouble-shooting for this particular message "nv1 = 140942,
nv1 = 143525", and I found out that "143525" was in the "base" folder
(kp5_base), and "140942" was for the two longitudinally registered images
(kp5.long.kp5_base, and kp5b.long.kp5_base).

The command line I used was : “long_mris_slopes --qdec
./qdec/AS_long_qdec.dat --meas thickness --hemi lh --do-avg --do-rate
--do-pc1 --do-spc --do-stack --do-label --time weeks –nosmooth”.

The first three lines in the qdec file:

“fsid fsid-base weeks age sex FSS avgPain

kp5 kp5_base 0 48 0 4.1 7

kp5b kp5_base 20 48 0 8.6 6”

This error was similar to what was in a previous post (
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024576.htmlby
joost janssen Jun 29, 2012). I tried to fix any similar problems, but
still wasn’t able to get it working.

What else could I have been doing wrong?

The on screen error output is provided as follows

Many thanks

Keith

Postdoctoral fellow
Toronto Western Hospital
Toronto, Ontario
Canada

***

Parsing the qdec table: ./qdec/AS_long_qdec.dat

Working in SUBJECTS_DIR:
/data/keith/freesurferdata/subjects_longitudinal_5.1_old

Subject-Template: kp5_base

INFO: 2 TPs in kp5_base , mean age: 10.0

===


SUBJECT kp5_base Intersecting Within-Subject Cortex Label

cp
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/label/lh.cortex.label
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label


mris_label_calc intersect
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/label/lh.cortex.label
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label


LabelWrite: saving to
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label


===


SUBJECT kp5_base Stackinbg Within-Subject Maps

mri_concat
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/surf/lh.thickness
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/surf/lh.thickness
--o
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh


ninputs = 2

Checking inputs

nframestot = 2

Allocing output

Done allocing

nframes = 2

Writing to
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh


===


SUBJECT kp5_base Running Within-Subject GLM

Writing ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat ...

mri_glmfit --y
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh
--X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat --allow-zero-dof
--no-contrasts-ok --surf kp5_base lh --label
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
--glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm

Reading source surface
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.white


Number of vertices 143525

Number of faces 287046

Total area 91438.851562

AvgVtxArea 0.637094

AvgVtxDist 0.873064

StdVtxDist 0.245806

$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $

cwd /data/keith/freesurferdata/subjects_longitudinal_5.1_old

cmdline mri_glmfit --y
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh
--X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat --allow-zero-dof
--no-contrasts-ok --surf kp5_base lh --label
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
--glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm

sysname Linux

hostname davissvr1.uhnres.utoronto.ca

machine x86_64

user qwu

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh


logyflag 0

X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat

usedti 0

labelmask
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label


maskinv 0

glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory ./tmp-kp5_base_lh_thickness_6PR2rH/glm

Loading y from
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thi

Re: [Freesurfer] Use our own training subjects?

[Susan Kuo]

Thank you, Anastasia. I think we can recruit some hard-working
neuroanatomists here to help us with the labeling. I believe I will give
this a shot for the IFO. Again, thanks for your support on this - I really
appreciate it!

Susie Kuo


On Wed, May 1, 2013 at 11:04 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Susan - Currently the only way to read in the manually labeled
> streamlines from the training subjects is in .trk format, which is what
> trackvis writes out. If you prefer to use another program for manual
> labeling, then its output would have to be converted to .trk format. This
> format is described in the online documentation for trackvis.
>
> The priors are generated by trac-all on the fly, given the .trk files and
> aparc+aseg for each of the training subjects. So once the manual labeling
> is done, it's just about transforming these files to the template space and
> passing the list to trac-all. I'm happy to document this part. The hard
> work is the manual labeling!
>
> Hope this helps,
> a.y
>
>
> On Wed, 1 May 2013, Susan Kuo wrote:
>
>  Hi Anastasia,  I would like to add several tracts of interest to our
>> priors, e.g. the IFO and sections of
>> the corpus callosum. Would it be possible for you to document how your
>> group created your priors? Are we
>> constrained to trackvis as a program? I know this is a lot of
>> documentation, but I would be happy to help.
>> I'm located on the NIH campus, and can travel up to help with the
>> documentation if you'd like. It would be
>> a good learning process for me. Thank you!
>>
>>
>> Susan Kuo
>>
>>
>> On Fri, Apr 26, 2013 at 1:42 PM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>   Hi Susie - If you can label the connection that you want in
>> trackvis consistently in a set of
>>   subjects, then yes, it'd be possible to create your own mini atlas.
>> You'd have to map the .trk
>>   files with the trackvis streamlines and the aparc+aseg's from all
>> the training subjects to
>>   either the MNI or the CVS template. Then there's a trainfile
>> variable that you can set in the
>>   configuration file that tells trac-all where to find the training
>> data. If you decide to go
>>   through with this, I can try to document it in more detail on the
>> wiki.
>>
>>   a.y
>>
>>   On Mon, 15 Apr 2013, Susan Kuo wrote:
>>
>> Hi Anastasia,
>>We were viewing the arcuate fasiculus tract created by
>> TRACULA, and noticed that
>> the tract did not reach
>> Broca's area. While there exists literature that now
>> challenges this
>> neuroanatomical convention, I would
>> like to investigate the possibility of creating and inputting
>> on our own training
>> subjects as priors. Do
>> you know if we can try this? Thank you!
>>
>> --
>> Susie Kuo
>>
>> Mediocrity knows nothing higher than itself, but talent
>> instantly recognizes
>> genius. - Sir Arthur Conan
>> Doyle, Sherlock Holmes- Valley of Fear
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> Susie Kuo
>>
>> Mediocrity knows nothing higher than itself, but talent instantly
>> recognizes genius. - Sir Arthur Conan
>> Doyle, Sherlock Holmes- Valley of Fear
>>
>>


-- 
Susie Kuo

Mediocrity knows nothing higher than itself, but talent instantly
recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of
Fear*
___
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.

Re: [Freesurfer] Which space is TRACULA statistics in?

[Susan Kuo]

Thank you, Anastasia! I will keep this in mind when I analyze the group
statistics.





On Wed, May 1, 2013 at 11:07 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Susan - All outputs of tracula are in native diffusion space.
> Tractography is performed in the native space, without any transformationon
> the DWIs to another space.
>
> a.y
>
>
> On Wed, 1 May 2013, Susan Kuo wrote:
>
>  Hi FreeSurfing researchers,   I am looking at the pathstats.overall.txt,
>> and wanted to see if anybody knew
>> which space these voxels are in - I assume MNI space (given that I used
>> the MNI template) and not
>> individual diffusion space, but would like to confirm. Does anybody know
>> for certain what space this data
>> is reported in?
>>
>>
>> Thanks!
>>
>> --
>> Susie Kuo
>>
>>
>>
>>
>>
>
> 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.
>



-- 
Susie Kuo

Mediocrity knows nothing higher than itself, but talent instantly
recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of
Fear*
___
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.

Re: [Freesurfer] Which space is TRACULA statistics in?

[Anastasia Yendiki]

Hi Susan - All outputs of tracula are in native diffusion space. 
Tractography is performed in the native space, without any 
transformationon the DWIs to another space.


a.y

On Wed, 1 May 2013, Susan Kuo wrote:


Hi FreeSurfing researchers,   I am looking at the pathstats.overall.txt, and 
wanted to see if anybody knew
which space these voxels are in - I assume MNI space (given that I used the MNI 
template) and not
individual diffusion space, but would like to confirm. Does anybody know for 
certain what space this data
is reported in? 


Thanks!

--
Susie Kuo



___
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.

Re: [Freesurfer] Use our own training subjects?

[Anastasia Yendiki]

Hi Susan - Currently the only way to read in the manually labeled 
streamlines from the training subjects is in .trk format, which is what 
trackvis writes out. If you prefer to use another program for manual 
labeling, then its output would have to be converted to .trk format. This 
format is described in the online documentation for trackvis.


The priors are generated by trac-all on the fly, given the .trk files and 
aparc+aseg for each of the training subjects. So once the manual labeling 
is done, it's just about transforming these files to the template space 
and passing the list to trac-all. I'm happy to document this part. The 
hard work is the manual labeling!


Hope this helps,
a.y

On Wed, 1 May 2013, Susan Kuo wrote:


Hi Anastasia,  I would like to add several tracts of interest to our priors, 
e.g. the IFO and sections of
the corpus callosum. Would it be possible for you to document how your group 
created your priors? Are we
constrained to trackvis as a program? I know this is a lot of documentation, 
but I would be happy to help.
I'm located on the NIH campus, and can travel up to help with the documentation 
if you'd like. It would be
a good learning process for me. Thank you!


Susan Kuo


On Fri, Apr 26, 2013 at 1:42 PM, Anastasia Yendiki 
 wrote:

  Hi Susie - If you can label the connection that you want in trackvis 
consistently in a set of
  subjects, then yes, it'd be possible to create your own mini atlas. You'd 
have to map the .trk
  files with the trackvis streamlines and the aparc+aseg's from all the 
training subjects to
  either the MNI or the CVS template. Then there's a trainfile variable 
that you can set in the
  configuration file that tells trac-all where to find the training data. 
If you decide to go
  through with this, I can try to document it in more detail on the wiki.

  a.y

  On Mon, 15 Apr 2013, Susan Kuo wrote:

Hi Anastasia, 
   We were viewing the arcuate fasiculus tract created by TRACULA, 
and noticed that
the tract did not reach
Broca's area. While there exists literature that now challenges this
neuroanatomical convention, I would
like to investigate the possibility of creating and inputting on 
our own training
subjects as priors. Do
you know if we can try this? Thank you!

--
Susie Kuo

Mediocrity knows nothing higher than itself, but talent instantly 
recognizes
genius. - Sir Arthur Conan
Doyle, Sherlock Holmes- Valley of Fear




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.




--
Susie Kuo

Mediocrity knows nothing higher than itself, but talent instantly recognizes 
genius. - Sir Arthur Conan
Doyle, Sherlock Holmes- Valley of Fear

___
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] Which space is TRACULA statistics in?

[Susan Kuo]

Hi FreeSurfing researchers,
  I am looking at the pathstats.overall.txt, and wanted to see if anybody
knew which space these voxels are in - I assume MNI space (given that I
used the MNI template) and not individual diffusion space, but would like
to confirm. Does anybody know for certain what space this data is reported
in?


Thanks!

-- 
Susie Kuo
___
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.

Re: [Freesurfer] How to flip L/R image in the freeview?

[Bruce Fischl]

Hi Glen

have you done the cross-hemisphere registration? If so, you can do this 
with mri_surf2surf, although the syntax is a bit tricky. Doug would know 
the details, but he's probably not going to be able to answer questions 
until tomorrow

cheers
Bruce
On Wed, 1 May 2013, Glen Lee wrote:


Freesurfer users, 
I'm a newbie for FS and have a rudimentary question for you. 

I have to overlay the group map for right hemisphere onto the lh.inflated
(due to using sym space, where left surface map became symmetrical to the
right), but I wonder if there is any way of reverting it back to rh.inflated
after the overlay using the freeview software. 

Your help would be appreciated. 
-Glen 





___
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.

Re: [Freesurfer] Visualize a fixed number of voxels using Tksurfer

[Bruce Fischl]

Hi Martin

I guess you could do this using the histogram in tksurfer (left and right 
clicking in it will set the min and max thresholds). Or it would be 
pretty easy in matlab.


cheers
Bruce
On Wed, 1 May 2013, Martin Bleichner wrote:


Hi all, 
is there a way to visualize a fixed number of voxesl using TKsurfer. I want
to display the 200 most active voxels (i.e. highest beta values) on the
inflated surface. Is there a possibility within tksurfer or do I have to
determine the corresponding threshold beforehand? 

Thanks
Martin

___
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.

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: incomplete tracts

[Bruce Fischl]

Hi Stefano

you need to tell us what command you were running.

cheers
Bruce

On Wed, 1 May 2013, 
std...@virgilio.it wrote:




I have this error:

writing registered surface 

to/Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_av

g35.sphere.reg...
expanding nbhd size to 1
1109: 1 negative triangles
mris_resample: Command not found.

Thanks,

Stefano

Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 30-apr-2013 21.12
A: 
Cc: 
Ogg: Re: [Freesurfer] R: Re:  R: Re:  R: Re:  incomplete tracts


Like I said in my previous email to you, please do not specify the CVS
template. This means delete the cvstempdir line from your configuration
file, or comment it out.

On Tue, 30 Apr 2013, std...@virgilio.it wrote:

> Hi Anastasia,
> when I run the configuration file (which I'm attaching)
> ERROR: Could not find CVS template
>
> I apologize but which is the correct directory of CVS template?
>
> Thanks,
>
>
> Stefano
>
>
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 26-apr-2013 20.08
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re:  R: Re:  incomplete tracts
>
>
> Hi Stefano - Just use the default for that, you don't need to specify the
> location.
>
> a.y
>
> On Sun, 21 Apr 2013, std...@virgilio.it wrote:
>
> > Hi Anastasia, 
> > I apologize but I do not find CVS template? Where it should be located?
> >
> > Thank you very much,
> >
> >
> > Stefano
> >
> >
> >
> > Messaggio originale
> > Da: ayend...@nmr.mgh.harvard.edu
> > Data: 9-apr-2013 17.50
> > A: 
> > Cc: 
> > Ogg: Re: [Freesurfer] R: Re:  incomplete tracts
> >
> >
> > Hi Stefano - Did you try CVS for the inter-subject registration? It
> > doesn't look like it from the configuration file.
> >
> > a.y
> >
> > On Tue, 9 Apr 2013, std...@virgilio.it wrote:
> >
> > > Hi Anastasia,
> > > yes, I tried.I'm attacking the last configuration file that I used.
> > >
> > > Thanks, 
> > >
> > >
> > > Stefano
> > >
> > > Messaggio originale
> > > Da: ayend...@nmr.mgh.harvard.edu
> > > Data: 9-apr-2013 1.42
> > > A: 
> > > Cc: 
> > > Ogg: Re: [Freesurfer] incomplete tracts
> > >
> > >
> > > What registration methods are you using for the intra-subject and
> > > inter-subject registration? Have you tried the different options?
> > >
> > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > >
> > > > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely
fminor.
> > > >
> > > > Messaggio originale
> > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > Data: 5-apr-2013 18.57
> > > > A: 
> > > > Cc: "freesurfer@nmr.mgh.harvard.edu"
> > > > Ogg: Re: [Freesurfer] R: Re: R: Re:  incomplete tracts
> > > >
> > > >
> > > > What you say "again" you mean with 5.2?
> > > >
> > > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > > >
> > > > > Hi Anastasia,
> > > > > yes, for some subject the low-b volume is in the end.
> > > > > Some subjects have again incomplete tracts.
> > > > > I'm attacking an example of configuration file that I'm using.
> > > > > I hope that you can check it please.
> > > > >
> > > > > Thanks,
> > > > >
> > > > >
> > > > > Stefano
> > > > >
> > > > > Messaggio originale
> > > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > > Data: 5-apr-2013 18.45
> > > > > A: 
> > > > > Cc:
"freesurfer@nmr.mgh.harvard.edu"
> > > > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts
> > > > >
> > > > >
> > > > > Hi Stefano - In your case we determined that the ones that had the
low-b
> > > > > volume in the end didn't run correctly, right? In that case, I
didn't
> > > need
> > > > > to see anything, you were going to try running 5.2.
> > > > >
> > > > > a.y
> > > > >
> > > > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > > > >
> > > > > > Hi Anastasia,
> > > > > > could I send you the data of a subject that I don't run
correctly? 
> > > > > >
> > > > > > I still have some subjects with tracts incomplete and I do not
know if
> > > > it depends
> > > > > from
> > > > > > my analysis or whether the images are not good.
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > >
> > > > > > Stefano
> > > > > >
> > > > > >
> > > > > > Messaggio originale
> > > > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > > > Data: 5-apr-2013 17.37
> > > > > > A: "Gerit Pfuhl"
> > > > > > Cc:
"freesurfer@nmr.mgh.harvard.edu"
> > > > > > Ogg: Re: [Freesurfer] incomplete tracts
> > > > > >
> > > > > >
> > > > > > Hi Gerit - If it's not an issue with the gradient table but
instead a
> > > > > > tractography initialization issue, I strongly recommend running
5.2
> > > with
> > > > > > bbregister for the registration (which is the default in 5.2
anyway).
> > > > > >
> > > > > > You can also upload an example data set with issues (include:
dmri,
> > > > > > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a
look:
> > > > > > https://gate.nmr.mgh.harvard.edu/filedrop2/
> > > > > >
> > > > > > Hope this helps,
> > > > > > a.y
> > > > > >
> > > > > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote:
> > > > > >

Re: [Freesurfer] setting up FS

[Bruce Fischl]

Hi Asha,

from the screen shot it looks like FS is installed properly. Have you 
tried running it? You could try:


tksurfer fsaverage lh inflated -curv

cheers
Bruce
On Wed, 1 May 2013, Ash Rafea wrote:


Hi there, I am totally a begginer in the Neurodebian "world" so please be
patient :(
I installed FS but I don't know how to setup freesurfer? I don't know how to
locate my FS home
Simply, I'm stuck at this step:
setenv FREESURFER_HOME /freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
 
attached is a screen shot of whats in my computer!

___
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] How to flip L/R image in the freeview?

[Glen Lee]

Freesurfer users,

I'm a newbie for FS and have a rudimentary question for you.

I have to overlay the group map for right hemisphere onto the lh.inflated
(due to using sym space, where left surface map became symmetrical to the
right), but I wonder if there is any way of reverting it back to
rh.inflated after the overlay using the freeview software.

Your help would be appreciated.
-Glen
___
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] Visualize a fixed number of voxels using Tksurfer

[Martin Bleichner]

Hi all,

is there a way to visualize a fixed number of voxesl using TKsurfer. I want
to display the 200 most active voxels (i.e. highest beta values) on the
inflated surface. Is there a possibility within tksurfer or do I have to
determine the corresponding threshold beforehand?

Thanks
Martin
___
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] R: Re: R: Re: R: Re: R: Re: incomplete tracts

[stdp82]

I have this error:
writing registered surface to 
/Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding
 nbhd size to 11109: 1 negative trianglesmris_resample: Command not found.
Thanks,
Stefano


Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 30-apr-2013 21.12
A: 
Cc: 
Ogg: Re: [Freesurfer] R: Re:  R: Re:  R: Re:  incomplete tracts


Like I said in my previous email to you, please do not specify the CVS 
template. This means delete the cvstempdir line from your configuration 
file, or comment it out.

On Tue, 30 Apr 2013, std...@virgilio.it wrote:

> Hi Anastasia,
> when I run the configuration file (which I'm attaching)
> ERROR: Could not find CVS template
> 
> I apologize but which is the correct directory of CVS template?
> 
> Thanks,
> 
> 
> Stefano
> 
> 
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 26-apr-2013 20.08
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re:  R: Re:  incomplete tracts
> 
> 
> Hi Stefano - Just use the default for that, you don't need to specify the
> location.
> 
> a.y
> 
> On Sun, 21 Apr 2013, std...@virgilio.it wrote:
> 
> > Hi Anastasia, 
> > I apologize but I do not find CVS template? Where it should be located?
> >
> > Thank you very much,
> >
> >
> > Stefano
> >
> >
> >
> > Messaggio originale
> > Da: ayend...@nmr.mgh.harvard.edu
> > Data: 9-apr-2013 17.50
> > A: 
> > Cc: 
> > Ogg: Re: [Freesurfer] R: Re:  incomplete tracts
> >
> >
> > Hi Stefano - Did you try CVS for the inter-subject registration? It
> > doesn't look like it from the configuration file.
> >
> > a.y
> >
> > On Tue, 9 Apr 2013, std...@virgilio.it wrote:
> >
> > > Hi Anastasia,
> > > yes, I tried.I'm attacking the last configuration file that I used.
> > >
> > > Thanks, 
> > >
> > >
> > > Stefano
> > >
> > > Messaggio originale
> > > Da: ayend...@nmr.mgh.harvard.edu
> > > Data: 9-apr-2013 1.42
> > > A: 
> > > Cc: 
> > > Ogg: Re: [Freesurfer] incomplete tracts
> > >
> > >
> > > What registration methods are you using for the intra-subject and
> > > inter-subject registration? Have you tried the different options?
> > >
> > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > >
> > > > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor.
> > > >
> > > > Messaggio originale
> > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > Data: 5-apr-2013 18.57
> > > > A: 
> > > > Cc: "freesurfer@nmr.mgh.harvard.edu"
> > > > Ogg: Re: [Freesurfer] R: Re: R: Re:  incomplete tracts
> > > >
> > > >
> > > > What you say "again" you mean with 5.2?
> > > >
> > > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > > >
> > > > > Hi Anastasia,
> > > > > yes, for some subject the low-b volume is in the end.
> > > > > Some subjects have again incomplete tracts.
> > > > > I'm attacking an example of configuration file that I'm using.
> > > > > I hope that you can check it please.
> > > > >
> > > > > Thanks,
> > > > >
> > > > >
> > > > > Stefano
> > > > >
> > > > > Messaggio originale
> > > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > > Data: 5-apr-2013 18.45
> > > > > A: 
> > > > > Cc: "freesurfer@nmr.mgh.harvard.edu"
> > > > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts
> > > > >
> > > > >
> > > > > Hi Stefano - In your case we determined that the ones that had the 
> > > > > low-b
> > > > > volume in the end didn't run correctly, right? In that case, I didn't
> > > need
> > > > > to see anything, you were going to try running 5.2.
> > > > >
> > > > > a.y
> > > > >
> > > > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > > > >
> > > > > > Hi Anastasia,
> > > > > > could I send you the data of a subject that I don't run correctly? 
> > > > > >
> > > > > > I still have some subjects with tracts incomplete and I do not know 
> > > > > > if
> > > > it depends
> > > > > from
> > > > > > my analysis or whether the images are not good.
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > >
> > > > > > Stefano
> > > > > >
> > > > > >
> > > > > > Messaggio originale
> > > > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > > > Data: 5-apr-2013 17.37
> > > > > > A: "Gerit Pfuhl"
> > > > > > Cc: "freesurfer@nmr.mgh.harvard.edu"
> > > > > > Ogg: Re: [Freesurfer] incomplete tracts
> > > > > >
> > > > > >
> > > > > > Hi Gerit - If it's not an issue with the gradient table but instead 
> > > > > > a
> > > > > > tractography initialization issue, I strongly recommend running 5.2
> > > with
> > > > > > bbregister for the registration (which is the default in 5.2 
> > > > > > anyway).
> > > > > >
> > > > > > You can also upload an example data set with issues (include: dmri,
> > > > > > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look:
> > > > > > https://gate.nmr.mgh.harvard.edu/filedrop2/
> > > > > >
> > > > > > Hope this helps,
> > > > > > a.y
> > > > > >
> > > > > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote:
> > > > > >
> > > > > > > Dear Anastasia,
> > > > > > >
> > > > > > > thanks for the

[Freesurfer] Begginer!

[Ash Rafea]

Hi there, I am totally a begginer in the Neurodebian "world" so please be
patient :(
I installed FS but I don't know how to setup freesurfer? I don't know how
to locate my FS home
Simply, I'm stuck at this step:
setenv FREESURFER_HOME /freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

any help?
___
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.