Hi everybody,
I am trying to process high res monkey scans in FreeSurfer (voxel size 0.31 x 1 x 0.31 mm). For converting them I use:
mri_convert rawdata.img orig.mgz -iis 0.31 -ijs 1 -iks 0.31 -cm
But I actually get a very small image in tkmedit. Further, moving each slice in any of the three directions give a volume index change of 1 and voxel RAS change of 3 (i.e. on the coronal slice number 128, the volume index 128 128 128 is equivalent to the volume RAS 0 0 0; going to the coronal slice 129 without moving the cursor will give the volume index 128 128 131, and RAS 0 1 0).
Since RAS are the coordinates in millimeter, I actually expected that any change of slice would be accompanied by a 0.31 change on RAS and variation of 1 on volume index... Is there any basic step that I missed?
Thank you very much,
Marie Schaer
Hi Marie,
try using scuba to view the data:
scuba -v orig.mgz
not sure if the .31mm orig.mgz will go through the recon okay. Currently people have to reset the dimensions to be 1mm (even though they are really res than that).
sorry, it's on our list of things to fix.
Bruce
On Wed, 2 Aug 2006, Marie Schaer wrote:
Hi everybody,
I am trying to process high res monkey scans in FreeSurfer (voxel size 0.31 x 1 x 0.31 mm). For converting them I use:
mri_convert rawdata.img orig.mgz -iis 0.31 -ijs 1 -iks 0.31 -cm
But I actually get a very small image in tkmedit. Further, moving each slice in any of the three directions give a volume index change of 1 and voxel RAS change of 3 (i.e. on the coronal slice number 128, the volume index 128 128 128 is equivalent to the volume RAS 0 0 0; going to the coronal slice 129 without moving the cursor will give the volume index 128 128 131, and RAS 0 1 0).
Since RAS are the coordinates in millimeter, I actually expected that any change of slice would be accompanied by a 0.31 change on RAS and variation of 1 on volume index... Is there any basic step that I missed?
Thank you very much,
Marie Schaer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Bruce, in scuba I can view the high-res orig.mgz.
As you pointed out, it is not simple to use recon-all with high-res images. Would you agree on the fact that all my thickness measurements will be overestimated by a factor (1 / 0.31) if I just process the 0.31mm images as if they were 1mm resolution? It should not affect group comparison but only absolute measurements. What is your opinion?
Thank you very much for your always helpful comments!
Marie
On Aug 2, 2006, at 8:43 PM, Bruce Fischl wrote:
Hi Marie,
try using scuba to view the data:
scuba -v orig.mgz
not sure if the .31mm orig.mgz will go through the recon okay. Currently people have to reset the dimensions to be 1mm (even though they are really res than that).
sorry, it's on our list of things to fix.
Bruce
On Wed, 2 Aug 2006, Marie Schaer wrote:
Hi everybody,
I am trying to process high res monkey scans in FreeSurfer (voxel size 0.31 x 1 x 0.31 mm). For converting them I use:
mri_convert rawdata.img orig.mgz -iis 0.31 -ijs 1 -iks 0.31 -cm
But I actually get a very small image in tkmedit. Further, moving each slice in any of the three directions give a volume index change of 1 and voxel RAS change of 3 (i.e. on the coronal slice number 128, the volume index 128 128 128 is equivalent to the volume RAS 0 0 0; going to the coronal slice 129 without moving the cursor will give the volume index 128 128 131, and RAS 0 1 0).
Since RAS are the coordinates in millimeter, I actually expected that any change of slice would be accompanied by a 0.31 change on RAS and variation of 1 on volume index... Is there any basic step that I missed?
Thank you very much,
Marie Schaer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, you'll need to correct them manually afterwards.
On Thu, 3 Aug 2006, Marie Schaer wrote:
Thanks Bruce, in scuba I can view the high-res orig.mgz.
As you pointed out, it is not simple to use recon-all with high-res images. Would you agree on the fact that all my thickness measurements will be overestimated by a factor (1 / 0.31) if I just process the 0.31mm images as if they were 1mm resolution? It should not affect group comparison but only absolute measurements. What is your opinion?
Thank you very much for your always helpful comments!
Marie
On Aug 2, 2006, at 8:43 PM, Bruce Fischl wrote:
Hi Marie,
try using scuba to view the data:
scuba -v orig.mgz
not sure if the .31mm orig.mgz will go through the recon okay. Currently people have to reset the dimensions to be 1mm (even though they are really res than that).
sorry, it's on our list of things to fix.
Bruce
On Wed, 2 Aug 2006, Marie Schaer wrote:
Hi everybody,
I am trying to process high res monkey scans in FreeSurfer (voxel size 0.31 x 1 x 0.31 mm). For converting them I use:
mri_convert rawdata.img orig.mgz -iis 0.31 -ijs 1 -iks 0.31 -cm
But I actually get a very small image in tkmedit. Further, moving each slice in any of the three directions give a volume index change of 1 and voxel RAS change of 3 (i.e. on the coronal slice number 128, the volume index 128 128 128 is equivalent to the volume RAS 0 0 0; going to the coronal slice 129 without moving the cursor will give the volume index 128 128 131, and RAS 0 1 0).
Since RAS are the coordinates in millimeter, I actually expected that any change of slice would be accompanied by a 0.31 change on RAS and variation of 1 on volume index... Is there any basic step that I missed?
Thank you very much,
Marie Schaer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Marie Schaer