Re: [Freesurfer] convert FS volume in scanner space

2015-07-09 Thread von Polier, Georg
Thanks for getting back. What I need is hippoSflabels in the original 
coordinates/space of the dicom-files (to compare with manual segmentation). 
Basically I had success with

mri_convert -rl rawavg.mgz -rt nearest lh.hippoSfLabels-T1.v10.mgz 
FS_outfile.nii

(identical dimensions, voxel spacing, origin and orientation) however, 
segmentation have wholes that renders shape analysis impossible. Running

mri_vol2vol --mov lh.hippoSfLabels-T1.v10.mgz --targ orig/001.mgz --regheader 
--o FS_outfile.nii --no-save-reg   (or —targ rawavg)

resulted in perfect segmentations, but the coordinates had (identical 
dimensions and voxel spacing) but different origin and orientation (dicom: AIL; 
FS_outfile: ASR) when I open both files in ITK Snap. Also, FS seems to involve 
more/ other steps in mri_vol2vol as compared to mri_convert. So I figured I 
would either need other commands for mri_vol2vol or an additional step to have 
my (perfect) segmention in dicom-coordinates. I tried

mri_convert FS_outfile.nii FS_outfile_LPS.nii --in_orientation RAS 
--out_orientation LPS

but the output was completely wrong oriented.

So that’s were I am stuck. Back to your question - I guess I need the 
voxel-to-RAS matrix to have FS-output in the original real world coordinates to 
enable direct comparisons and then guidance on how to calculate the image 
translations with FS (on a larger data set).



Am 09.07.2015 um 19:00 schrieb Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu:

There are a lot of details here that can easily get confused. The pixel
data are not in any particular space. The order of the pixel data are
not changed when converted to mgz. The direction cosines that indicate
how to convert a col-row-slice to a real world coordinate dictate how
the pixels are displayed or interpreted spatially. The direction cosines
in the dicom file will be LPS. The direction cosines in RAS space are
computed and saved in the mgz file. The coordinate center will not
change. Thus if you use the voxel-to-RAS matrix to compute the location
in the scanner of a given col-row-slice, it will do so accurately.

Given that, can you explain more about what you actually need?



On 07/08/2015 10:51 AM, von Polier, Georg wrote:
Sorry for the confusion: According to the presentation fswiki/CoordinateSystems 
(below) I meant, the data are in native space/ RAS, with coordinate center not 
at magnet center, which is what I need.

Scanner Space - coordinate center at magnet isocenter, bore axis is Z, X to the 
left, Y to the ceiling. Direction cosines and P0 defined in DICOM file (note: 
this is an LPS, not RAS coordinate system)  Native - basically the same as 
scanner, but RAS.

-Ursprüngliche Nachricht-
Von: 
freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve
Gesendet: Mittwoch, 8. Juli 2015 16:37
An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] convert FS volume in scanner space

what do you mean the coords are still in RAS?

On 7/8/15 8:25 AM, von Polier, Georg wrote:
My command line was

cd $SUBJECTS_DIR/subjid/mri
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o
brain-in-rawavg.mgz --no-save-reg

according to   fswiki/FsAnat-to-NativeAnat.

As I mentioned, I am happy with the results but the coordinates are still RAS 
(from my understanding) and different from the original dicom-coordinates (that 
my manual segmentations are in). When I use mri_convert, the coordinates are in 
dicom-space (0 in center of image/ coil; offset and z-axis identical with 
original dicoms), but the segmentation seems different/ more prone to 
artifacts, also when I use rt- nearest.

Georg

-Ursprüngliche Nachricht-
Von: 
freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas
Greve
Gesendet: Mittwoch, 8. Juli 2015 04:20
An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] convert FS volume in scanner space

what was your vol2vol command line? What wiki page were you referencing?
What was the problem with the coordinates?

On 7/7/15 8:11 PM, Bruce Fischl wrote:
I think you meant you want nearest neighbor interpolation, not
trilinear, since you are mapping labels. Try using -rt nearest insted
On Wed, 8 Jul 2015, von Polier, Georg wrote:

Thanks for your reply. I tried mri_convert with -rt interpolate (resulting in 
trilinear interpolation), however, the results were partially prone to 
artifacts and different from those I get with mir_vol2vol (but in dicom space).

Is there a way using mir_vol2vol with results in dicom space, or a second step 
that gives a vox2vox from conformed/anatomical space to dicom space?

I use the .mgz-output of hippo_subfields (FS_dev).

Thanks again,
Georg



Am 07.07.2015 um 02:34

Re: [Freesurfer] convert FS volume in scanner space

2015-07-09 Thread von Polier, Georg
Different in nii: type: FLOAT (3); TE, TI, flip angle: 0; PhEncDir: Unknown;

xform info, voxel to ras transform, ras to voxel identical

Loading rawavg.nii and FS_outfile.nii in ITK looks in perfect alignment, it 
says orientation of FS_outfile is Oblique (closest to ASR);
When I load the manual segents, (into rawavg) it warns of header mismatch 
(orientation ASL) and I notice a slight shift.

Loading the FS_outfile into the original dicom-file, it equally warns of header 
missmatch, I notice a slight shift.





Volume information for rawavg.mgz

  type: MGH

dimensions: 256 x 256 x 176

   voxel sizes: 0.9766, 0.9766, 1.

  type: SHORT (4)

   fov: 250.000

   dof: 0

xstart: -125.0, xend: 125.0

ystart: -125.0, yend: 125.0

zstart: -88.0, zend: 88.0

TR: 1900.00 msec, TE: 2.52 msec, TI: 900.00 msec, flip angle: 9.00 
degrees

   nframes: 1

   PhEncDir: ROW

ras xform present

xform info: x_r =  -0.0332, y_r =  -0.0628, z_r =  -0.9975, c_r =-3.9057

  : x_a =  -0.9995, y_a =   0.0021, z_a =   0.0331, c_a =14.5730

  : x_s =   0., y_s =  -0.9980, z_s =   0.0628, c_s =   -24.5551


talairach xfm :

Orientation   : PIL

Primary Slice Direction: sagittal


voxel to ras transform:

   -0.0324  -0.0613  -0.997595.8613

   -0.9760   0.0020   0.0331   136.3322

0.  -0.9746   0.062894.6727

0.   0.   0. 1.


voxel-to-ras determinant -0.953674


ras to voxel transform:

   -0.0340  -1.0234   0.   142.7820

   -0.0643   0.0021  -1.0220   102.6232

   -0.9975   0.0331   0.062885.1638

0.   0.   0. 1.


Volume information for FS_output.nii
  type: nii
dimensions: 256 x 256 x 176
   voxel sizes: 0.9766, 0.9766, 1.
  type: FLOAT (3)
   fov: 250.000
   dof: 0
xstart: -125.0, xend: 125.0
ystart: -125.0, yend: 125.0
zstart: -88.0, zend: 88.0
TR: 1900.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -0.0332, y_r =  -0.0628, z_r =  -0.9975, c_r =-3.9057
  : x_a =  -0.9995, y_a =   0.0021, z_a =   0.0331, c_a =14.5730
  : x_s =   0., y_s =  -0.9980, z_s =   0.0628, c_s =   -24.5551
Orientation   : PIL
Primary Slice Direction: sagittal

voxel to ras transform:
   -0.0324  -0.0613  -0.997595.8613
   -0.9760   0.0020   0.0331   136.3322
0.  -0.9746   0.062894.6727
0.   0.   0. 1.

voxel-to-ras determinant -0.953674

ras to voxel transform:
   -0.0340  -1.0234   0.   142.7820
   -0.0643   0.0021  -1.0220   102.6232
   -0.9975   0.0331   0.062885.1638
0.   0.   0. 1.



Am 09.07.2015 um 20:54 schrieb Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu:

vol2vol is the right way to go on this. When you run mri_info on
rawavg.mgz and FS_outfile.nii, do they have the same geometry? What if
you convert rawavg.mgz to nii and open it and outfile.nii in ITK Snap,
so they look the same?

On 07/09/2015 02:44 PM, von Polier, Georg wrote:
Thanks for getting back. What I need is hippoSflabels in the original
coordinates/space of the dicom-files (to compare with manual
segmentation). Basically I had success with
mri_convert -rl rawavg.mgz -rt nearest lh.hippoSfLabels-T1.v10.mgz  
FS_outfile.nii
(identical dimensions, voxel spacing, origin and orientation) however,
segmentation have wholes that renders shape analysis impossible. Running

mri_vol2vol --mov lh.hippoSfLabels-T1.v10.mgz --targ orig/001.mgz
--regheader --o FS_outfile.nii --no-save-reg   (or —targ rawavg)

resulted in perfect segmentations, but the coordinates had (identical
dimensions and voxel spacing) but different origin and orientation
(dicom: AIL; FS_outfile: ASR) when I open both files in ITK Snap.
Also, FS seems to involve more/ other steps in mri_vol2vol as compared
to mri_convert. So I figured I would either need other commands for
mri_vol2vol or an additional step to have my (perfect) segmention in
dicom-coordinates. I tried

mri_convert FS_outfile.nii FS_outfile_LPS.nii --in_orientation RAS
--out_orientation LPS

but the output was completely wrong oriented.

So that’s were I am stuck. Back to your question - I guess I need the
voxel-to-RAS matrix to have FS-output in the original real world
coordinates to enable direct comparisons and then guidance on how to
calculate the image translations with FS (on a larger data set).



Am 09.07.2015 um 19:00 schrieb Douglas N Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu:

There are a lot

Re: [Freesurfer] convert FS volume in scanner space

2015-07-09 Thread von Polier, Georg
The vol that holds the man segs was created by ITK Snap; your command line 
worked for me, THANKS SO MUCH!!
Georg

 Am 09.07.2015 um 22:12 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:
 
 How was the volume that holds the manual segs created? Another thing you 
 can try is
 
 mri_vol2vol --mov lh.hippoSfLabels-T1.v10.mgz --targ mansegs.nii 
 --regheader --o FS_outfile.nii
 
 
 
 
 On 07/09/2015 03:59 PM, von Polier, Georg wrote:
 
 Different in nii: type: FLOAT (3); TE, TI, flip angle: 0; PhEncDir: 
 Unknown;
 
 xform info, voxel to ras transform, ras to voxel identical
 
 
 Loading rawavg.nii and FS_outfile.nii in ITK looks in perfect 
 alignment, it says orientation of FS_outfile is Oblique (closest to ASR);
 When I load the manual segents, (into rawavg) it warns of header 
 mismatch (orientation ASL) and I notice a slight shift.
 
 Loading the FS_outfile into the original dicom-file, it equally warns 
 of header missmatch, I notice a slight shift.
 
 
 
 
 Volume information for rawavg.mgz
 
 type: MGH
 
 dimensions: 256 x 256 x 176
 
   voxel sizes: 0.9766, 0.9766, 1.
 
 type: SHORT (4)
 
 fov: 250.000
 
 dof: 0
 
 xstart: -125.0, xend: 125.0
 
 ystart: -125.0, yend: 125.0
 
 zstart: -88.0, zend: 88.0
 
 TR: 1900.00 msec, TE: 2.52 msec, TI: 900.00 msec, flip angle: 9.00 degrees
 
 nframes: 1
 
 PhEncDir: ROW
 
 ras xform present
 
xform info: x_r =  -0.0332, y_r =  -0.0628, z_r =  -0.9975, c_r = 
 -3.9057
 
  : x_a =  -0.9995, y_a =   0.0021, z_a =   0.0331, c_a = 14.5730
 
  : x_s =   0., y_s =  -0.9980, z_s =   0.0628, c_s = -24.5551
 
 
 talairach xfm :
 
 Orientation   : PIL
 
 Primary Slice Direction: sagittal
 
 
 voxel to ras transform:
 
-0.0324  -0.0613  -0.997595.8613
 
-0.9760   0.0020   0.0331   136.3322
 
0.  -0.9746   0.062894.6727
 
0.   0.   0. 1.
 
 
 voxel-to-ras determinant -0.953674
 
 
 ras to voxel transform:
 
-0.0340  -1.0234   0.   142.7820
 
-0.0643   0.0021  -1.0220   102.6232
 
-0.9975   0.0331   0.062885.1638
 
0.   0.   0. 1.
 
 
 
 Volume information for FS_output.nii
 type: nii
 dimensions: 256 x 256 x 176
   voxel sizes: 0.9766, 0.9766, 1.
 type: FLOAT (3)
  fov: 250.000
  dof: 0
 xstart: -125.0, xend: 125.0
 ystart: -125.0, yend: 125.0
 zstart: -88.0, zend: 88.0
  TR: 1900.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
 nframes: 1
 PhEncDir: UNKNOWN
 ras xform present
xform info: x_r =  -0.0332, y_r =  -0.0628, z_r =  -0.9975, c_r = 
 -3.9057
: x_a =  -0.9995, y_a =   0.0021, z_a =   0.0331, c_a = 14.5730
: x_s =   0., y_s =  -0.9980, z_s =   0.0628, c_s = -24.5551
 Orientation   : PIL
 Primary Slice Direction: sagittal
 
 voxel to ras transform:
  -0.0324  -0.0613  -0.997595.8613
  -0.9760   0.0020   0.0331   136.3322
  0.  -0.9746   0.062894.6727
  0.   0.   0. 1.
 
 voxel-to-ras determinant -0.953674
 
 ras to voxel transform:
  -0.0340  -1.0234   0.   142.7820
  -0.0643   0.0021  -1.0220   102.6232
  -0.9975   0.0331   0.062885.1638
  0.   0.   0. 1.
 
 
 
 Am 09.07.2015 um 20:54 schrieb Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu:
 
 vol2vol is the right way to go on this. When you run mri_info on
 rawavg.mgz and FS_outfile.nii, do they have the same geometry? What if
 you convert rawavg.mgz to nii and open it and outfile.nii in ITK Snap,
 so they look the same?
 
 On 07/09/2015 02:44 PM, von Polier, Georg wrote:
 Thanks for getting back. What I need is hippoSflabels in the original
 coordinates/space of the dicom-files (to compare with manual
 segmentation). Basically I had success with
 mri_convert -rl rawavg.mgz -rt nearest lh.hippoSfLabels-T1.v10.mgz 
 FS_outfile.nii
 (identical dimensions, voxel spacing, origin and orientation) however,
 segmentation have wholes that renders shape analysis impossible. Running
 
 mri_vol2vol --mov lh.hippoSfLabels-T1.v10.mgz --targ orig/001.mgz
 --regheader --o FS_outfile.nii --no-save-reg   (or —targ rawavg)
 
 resulted in perfect segmentations, but the coordinates had (identical
 dimensions and voxel spacing) but different origin and orientation
 (dicom: AIL; FS_outfile: ASR) when I open both files in ITK Snap.
 Also, FS seems to involve more/ other steps in mri_vol2vol as compared
 to mri_convert. So I figured I would either need other commands for
 mri_vol2vol or an additional step to have my (perfect) segmention in
 dicom-coordinates. I tried
 
 mri_convert FS_outfile.nii FS_outfile_LPS.nii --in_orientation RAS
 --out_orientation LPS
 
 but the output was completely wrong oriented.
 
 So that’s were I am stuck. Back to your question - I guess I need the
 voxel-to-RAS matrix to have FS-output in the original real world
 coordinates to enable direct comparisons and then guidance on how to
 calculate the image translations with FS (on a larger data set

Re: [Freesurfer] convert FS volume in scanner space

2015-07-08 Thread von Polier, Georg
My command line was 

cd $SUBJECTS_DIR/subjid/mri
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o 
brain-in-rawavg.mgz --no-save-reg  

according to   fswiki/FsAnat-to-NativeAnat. 

As I mentioned, I am happy with the results but the coordinates are still RAS 
(from my understanding) and different from the original dicom-coordinates (that 
my manual segmentations are in). When I use mri_convert, the coordinates are in 
dicom-space (0 in center of image/ coil; offset and z-axis identical with 
original dicoms), but the segmentation seems different/ more prone to 
artifacts, also when I use rt- nearest. 

Georg

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve
Gesendet: Mittwoch, 8. Juli 2015 04:20
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] convert FS volume in scanner space

what was your vol2vol command line? What wiki page were you referencing? 
What was the problem with the coordinates?

On 7/7/15 8:11 PM, Bruce Fischl wrote:
 I think you meant you want nearest neighbor interpolation, not 
 trilinear, since you are mapping labels. Try using -rt nearest insted 
 On Wed, 8 Jul 2015, von Polier, Georg wrote:

 Thanks for your reply. I tried mri_convert with -rt interpolate (resulting 
 in trilinear interpolation), however, the results were partially prone to 
 artifacts and different from those I get with mir_vol2vol (but in dicom 
 space).

 Is there a way using mir_vol2vol with results in dicom space, or a second 
 step that gives a vox2vox from conformed/anatomical space to dicom space?

 I use the .mgz-output of hippo_subfields (FS_dev).

 Thanks again,
 Georg



 Am 07.07.2015 um 02:34 schrieb Bruce Fischl fis...@nmr.mgh.harvard.edu:

 Hi Georg

 if you have a volume (like the 001.mgz) that is in scanner 
 coordinates you can use the reslice like and resample type flags in 
 mri_convert:

 mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz

 cheers
 Bruce

 On Mon, 6 Jul 2015, von
 Polier, Georg wrote:

 Dear FreeSurfers,

 I need to convert an FS-volume back in scanner space (to calculate overlap 
 with manual segmentation).
 I went through the wiki-entry and converted to native space with 
 mir_vol2vol, however the coordinates are still RAS and not identical with 
 the original Scanner-coordinates. I tried mri_convert, however, the 
 results were not as good as mri_vol2vol (apparently need trilinear 
 interpolation, not available in mri_convert).

 Any help would be greatly appreciated,

 Cheers, Georg
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Re: [Freesurfer] convert FS volume in scanner space

2015-07-07 Thread von Polier, Georg
Thanks for your reply. I tried mri_convert with -rt interpolate (resulting in 
trilinear interpolation), however, the results were partially prone to 
artifacts and different from those I get with mir_vol2vol (but in dicom space). 

Is there a way using mir_vol2vol with results in dicom space, or a second step 
that gives a vox2vox from conformed/anatomical space to dicom space?

I use the .mgz-output of hippo_subfields (FS_dev). 

Thanks again, 
Georg



 Am 07.07.2015 um 02:34 schrieb Bruce Fischl fis...@nmr.mgh.harvard.edu:
 
 Hi Georg
 
 if you have a volume (like the 001.mgz) that is in scanner coordinates 
 you can use the reslice like and resample type flags in mri_convert:
 
 mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz
 
 cheers
 Bruce
 
 On Mon, 6 Jul 2015, von 
 Polier, Georg wrote:
 
 Dear FreeSurfers,
 
 I need to convert an FS-volume back in scanner space (to calculate overlap 
 with manual segmentation).
 I went through the wiki-entry and converted to native space with 
 mir_vol2vol, however the coordinates are still RAS and not identical with 
 the original Scanner-coordinates. I tried mri_convert, however, the results 
 were not as good as mri_vol2vol (apparently need trilinear interpolation, 
 not available in mri_convert).
 
 Any help would be greatly appreciated,
 
 Cheers, Georg
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
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 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.
 


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[Freesurfer] convert FS volume in scanner space

2015-07-06 Thread von Polier, Georg
Dear FreeSurfers, 

I need to convert an FS-volume back in scanner space (to calculate overlap with 
manual segmentation). 
I went through the wiki-entry and converted to native space with mir_vol2vol, 
however the coordinates are still RAS and not identical with the original 
Scanner-coordinates. I tried mri_convert, however, the results were not as good 
as mri_vol2vol (apparently need trilinear interpolation, not available in 
mri_convert). 

Any help would be greatly appreciated, 

Cheers, Georg
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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.



[Freesurfer] Hippocampal subfields

2014-12-02 Thread von Polier, Georg Ferdinand Anto
Dear FreeSurfers,

I am just finishing a paper using output from Hippocampal subfields and 
recognized that the current version has been deprecated. I am interested in 
volumes of the whole hippocampus.
Are these volumes still valid and can you estimate when a new version will be 
available? Can you provide maybe a brief comment on the decision to deprecate 
the current version?
Best regards,
Georg

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


[Freesurfer] freeview and wm-segmentation errors

2011-05-31 Thread von Polier, Georg Ferdinand Anto
Hi,

using FS 5.1 now, I encountered two problems: 

1. when I try to start freeview on my personal laptop, this errors appears: 

[georg@localhost ~]$ freeview
freeview.bin: error while loading shared libraries: libXss.so.1: cannot open 
shared object file: No such file or directory

However,  libXss.so.1 is installed on my system running linux (Fedora 15). Do 
you habe any idea?


2. Running recon-all with -all flag on a cluster (Linux CentOs 5.6) the stream 
finishes with errors repeatedly showing this message: 

#@# WM Segmentation Tue May 31 12:36:00 CEST 2011

 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 

znzTAGskip: tag=544043625, failed to calloc 1952413696 bytes!


$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /rwthfs/rz/cluster/work/gg855262/subjects_AN/4550/mri
cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count 
wm255.txt 
sysname  Linux

input  wm.mgz
frame  0
nErode3d   0
nErode2d   0
output wm255.mgz
Binarizing based on threshold
min255
max255
binval1
binvalnot 0
Cannot allocate memory

recon-all -s 4550 exited with ERRORS at Tue May 31 12:36:01 CEST 2011


--
| Execution of Batch-Request stopped at Tue May 31 12:36:01 CEST 2011
| peak memory value: 2.386G
| real time used: 04:58:38

I did allocate 4 GB of memory and did not face this error when using FS 5.0 or 
FS 5.1-beta-release with same settings. 

Any recommendations? 
Thanks, Georg
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