Falk, it looks like that file was somehow converted to DOS. try:
dos2unix recon-all chmod a+x recon-all
then re-run
doug
On Mon, 6 Apr 2009, Falk Lüsebrink wrote:
Hi Nick,
I tried using your modified recon-all today but as soon as I try to process any data I receive following error message:
'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...].
Also it doesn't matter at all which flags I add to recon-all or if I don't use any flags at all, the error is the same. The unmodified recon-all performs well.
Regards, Falk
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: Thursday, April 02, 2009 3:28 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data
Falk,
There are no plans in the near future, but in the long term we'd like to remove the dependence on conforming the data.
It just occurred to me that you could have the best of both worlds: first run your data through the normal stream (conforming) up through autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same resolution as that created using the -hires stream, and copy it over. At least that would eliminate having to edit the original hires brainmask, which would save hours of work. If i get few minutes i will try this.
You can copy that recon-all over top your existing v4.x freesurfer installation (attached again for the list).
Nick
On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote:
Hi Nick,
Thank you very much. I'll have to look into that and try to process some other volumes which might work a bit better, with less manual intervention.
Are there any plans to improve Freesurfer in the (near) future so that hires data can be processed within the currently available stream?
Regards, Falk
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wednesday, April 01, 2009 7:53 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Measuring cortical thickness with high resolution data
Falk,
Attached is a modified recon-all script where I've added a -hires switch to force the stream to not conform the data to 1mm^3, and to not use the atlases.
Note that you should add the -clean flag to delete any work that had been done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz).
However, in working with the .8mm data that you sent me, working with hires data will require quite a bit of manual intervention due to the fact that the atlases normally used cannot be used. The first problem occurs in skull-stripping, where quite a bit of dura and skull remains, and seems to have intensity values close to gray matter. This would have to be manually erased on each of the slices. If it is not erased (I did not do this because of the amount of time required), then the wm.mgz file, which is what is tessellated to create the initial surface, will be very wrong (it tessellates the garbage surrounding the gray matter).
See also Bruce's prior posting on the problems of working with hires data in freesurfer.
Nick
On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote:
Hi Freesurfers,
Iÿÿm trying to evaluate the usefulness of high resolution scans acquired at 7T with an isometric voxel size of .6mm for the measurement of cortical thickness. The inhomogeneities are taken care of by dividing the scans with another scan of another sequence, so they are not an issue anymore.
My problem is that Freesurfer usually conforms the voxel size to 1mm which is not desirable. I tried using the ÿÿcm and ÿÿnoaseg flags for the recon-all process to avoid the conformation and to skip the subcortical segmentation, but another problem arises while using these flags.
The error I receive is occurring after the WM Segmentation and states as follows:
#--------------------------------------------
#...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009
cp wm.mgz wm.seg.mgz
mri_segment -keep brain.mgz wm.seg.mgz
preserving editing changes in output volume...
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0]
GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0]
setting bottom of white matter range to 77.9
setting top of gray matter range to 89.4
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
thickening thin strands....
20 segments, 4813 filled
10270 bright non-wm voxels segmented.
5589 diagonally connected voxels added...
white matter segmentation took 2.4 minutes
writing output to wm.seg.mgz...
ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 height=320.
The dimensions of the data Iÿÿm trying to process is 320 x 320 x 224 and is changed to 320 x 320 x 320 while using the ÿÿcm flag. It seems the mri_segment process canÿÿt handle any dimensions above 256 or Iÿÿm missing another flag.
Does someone has any ideas about that issue?
Regards,
Falk
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
Hi Doug,
Thanks! Now recon-all is processing well.
Regards, Falk
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, April 06, 2009 6:25 PM To: Falk Lüsebrink Cc: 'Nick Schmansky'; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data
Falk, it looks like that file was somehow converted to DOS. try:
dos2unix recon-all chmod a+x recon-all
then re-run
doug
On Mon, 6 Apr 2009, Falk Lüsebrink wrote:
Hi Nick,
I tried using your modified recon-all today but as soon as I try to
process any data I receive following error message:
'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...].
Also it doesn't matter at all which flags I add to recon-all or if I don't
use any flags at all, the error is the same. The unmodified recon-all performs well.
Regards, Falk
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu
[mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky
Sent: Thursday, April 02, 2009 3:28 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] Measuring cortical thickness with high
resolution data
Falk,
There are no plans in the near future, but in the long term we'd like to
remove the dependence on conforming the data.
It just occurred to me that you could have the best of both worlds: first run your data through the normal stream (conforming) up through
autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same resolution as that created using the -hires stream, and copy it over.
At least that would eliminate having to edit the original hires brainmask,
which would save hours of work. If i get few minutes i will try this.
You can copy that recon-all over top your existing v4.x freesurfer
installation (attached again for the list).
Nick
On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote:
Hi Nick,
Thank you very much. I'll have to look into that and try to process some
other volumes which might work a bit better, with less manual intervention.
Are there any plans to improve Freesurfer in the (near) future so that
hires data can be processed within the currently available stream?
Regards, Falk
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wednesday, April 01, 2009 7:53 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Measuring cortical thickness with high resolution data
Falk,
Attached is a modified recon-all script where I've added a -hires switch
to force the stream to not conform the data to 1mm^3, and to not use the atlases.
Note that you should add the -clean flag to delete any work that had been
done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz).
However, in working with the .8mm data that you sent me, working with
hires data will require quite a bit of manual intervention due to the fact that the atlases normally used cannot be used. The first problem occurs in skull-stripping, where quite a bit of dura and skull remains, and seems to have intensity values close to gray matter. This would have to be manually erased on each of the slices. If it is not erased (I did not do this because of the amount of time required), then the wm.mgz file, which is what is tessellated to create the initial surface, will be very wrong (it tessellates the garbage surrounding the gray matter).
See also Bruce's prior posting on the problems of working with hires data
in freesurfer.
Nick
On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote:
Hi Freesurfers,
Iÿÿm trying to evaluate the usefulness of high resolution scans acquired at 7T with an isometric voxel size of .6mm for the measurement of cortical thickness. The inhomogeneities are taken care of by dividing the scans with another scan of another sequence, so they are not an issue anymore.
My problem is that Freesurfer usually conforms the voxel size to 1mm which is not desirable. I tried using the ÿÿcm and ÿÿnoaseg flags for the recon-all process to avoid the conformation and to skip the subcortical segmentation, but another problem arises while using these flags.
The error I receive is occurring after the WM Segmentation and states as follows:
#--------------------------------------------
#...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009
cp wm.mgz wm.seg.mgz
mri_segment -keep brain.mgz wm.seg.mgz
preserving editing changes in output volume...
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0]
GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0]
setting bottom of white matter range to 77.9
setting top of gray matter range to 89.4
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
thickening thin strands....
20 segments, 4813 filled
10270 bright non-wm voxels segmented.
5589 diagonally connected voxels added...
white matter segmentation took 2.4 minutes
writing output to wm.seg.mgz...
ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 height=320.
The dimensions of the data Iÿÿm trying to process is 320 x 320 x 224 and is changed to 320 x 320 x 320 while using the ÿÿcm flag. It seems the mri_segment process canÿÿt handle any dimensions above 256 or Iÿÿm missing another flag.
Does someone has any ideas about that issue?
Regards,
Falk
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
Hi Nick,
First I wanted to give you a little bit of feedback. I'm still processing one volume with .6mm which is working perfectly fine until now. The skull stripping was done really well and no manual intervention was needed. I'm currently running autorecon3 and will have a look at the final results pretty soon. Thanks again for your modification and the help you offered.
But I recently tried to process the data I send to you simultaneously to see the results of the erroneous segmentation for myself. I just ran autorecon1 to view the brainmask.mgz and the result isn't as bad as the one you send to me in terms of remaining dura and skull, but only the right hemisphere is being shown and a small piece on the anterior is missing.
I also created a new subject so no older files could somehow influence the new process. The result is the same. The flags I used were simply -hires and -autorecon1 (and -clean in case for the older subject), so I don't know what might have caused this issue.
Regards, Falk
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve Sent: Monday, April 06, 2009 6:25 PM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu; 'Nick Schmansky' Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data
Falk, it looks like that file was somehow converted to DOS. try:
dos2unix recon-all chmod a+x recon-all
then re-run
doug
On Mon, 6 Apr 2009, Falk Lüsebrink wrote:
Hi Nick,
I tried using your modified recon-all today but as soon as I try to
process any data I receive following error message:
'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...].
Also it doesn't matter at all which flags I add to recon-all or if I don't
use any flags at all, the error is the same. The unmodified recon-all performs well.
Regards, Falk
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: Thursday, April 02, 2009 3:28 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data
Falk,
There are no plans in the near future, but in the long term we'd like to
remove the dependence on conforming the data.
It just occurred to me that you could have the best of both worlds: first run your data through the normal stream (conforming) up through
autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same resolution as that created using the -hires stream, and copy it over.
At least that would eliminate having to edit the original hires brainmask,
which would save hours of work. If i get few minutes i will try this.
You can copy that recon-all over top your existing v4.x freesurfer
installation (attached again for the list).
Nick
On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote:
Hi Nick,
Thank you very much. I'll have to look into that and try to process some
other volumes which might work a bit better, with less manual intervention.
Are there any plans to improve Freesurfer in the (near) future so that
hires data can be processed within the currently available stream?
Regards, Falk
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wednesday, April 01, 2009 7:53 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Measuring cortical thickness with high resolution data
Falk,
Attached is a modified recon-all script where I've added a -hires switch
to force the stream to not conform the data to 1mm^3, and to not use the atlases.
Note that you should add the -clean flag to delete any work that had been
done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz).
However, in working with the .8mm data that you sent me, working with
hires data will require quite a bit of manual intervention due to the fact that the atlases normally used cannot be used. The first problem occurs in skull-stripping, where quite a bit of dura and skull remains, and seems to have intensity values close to gray matter. This would have to be manually erased on each of the slices. If it is not erased (I did not do this because of the amount of time required), then the wm.mgz file, which is what is tessellated to create the initial surface, will be very wrong (it tessellates the garbage surrounding the gray matter).
See also Bruce's prior posting on the problems of working with hires data
in freesurfer.
Nick
On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote:
Hi Freesurfers,
Iÿÿm trying to evaluate the usefulness of high resolution scans acquired at 7T with an isometric voxel size of .6mm for the measurement of cortical thickness. The inhomogeneities are taken care of by dividing the scans with another scan of another sequence, so they are not an issue anymore.
My problem is that Freesurfer usually conforms the voxel size to 1mm which is not desirable. I tried using the ÿÿcm and ÿÿnoaseg flags for the recon-all process to avoid the conformation and to skip the subcortical segmentation, but another problem arises while using these flags.
The error I receive is occurring after the WM Segmentation and states as follows:
#--------------------------------------------
#...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009
cp wm.mgz wm.seg.mgz
mri_segment -keep brain.mgz wm.seg.mgz
preserving editing changes in output volume...
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0]
GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0]
setting bottom of white matter range to 77.9
setting top of gray matter range to 89.4
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
thickening thin strands....
20 segments, 4813 filled
10270 bright non-wm voxels segmented.
5589 diagonally connected voxels added...
white matter segmentation took 2.4 minutes
writing output to wm.seg.mgz...
ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 height=320.
The dimensions of the data Iÿÿm trying to process is 320 x 320 x 224 and is changed to 320 x 320 x 320 while using the ÿÿcm flag. It seems the mri_segment process canÿÿt handle any dimensions above 256 or Iÿÿm missing another flag.
Does someone has any ideas about that issue?
Regards,
Falk
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Falk Lüsebrink