Falk, Because the -hires switch disables the use the atlas during the skull- strip step, skull-stripping is more subject to stripping too much or too little brain (which is why use of the atlas was introduced). See this tutorial for ways to correct badly stripped skull:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix I had to add the switch -wsthresh 30 to get your sample subject to skull-strip (although it still left bits and pieces which affected the white matter tesselation step). Nick On Wed, 2009-04-08 at 15:07 +0200, Falk Lüsebrink wrote: > 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-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu > > [mailto:freesurfer-boun...@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:ni...@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 > gr...@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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
