Hi, I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in Freeview: mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o mask_in_Native.nii --mni152reg The overlay of the mask on f.nii in Freeview is mostly outside the brain.
How can I go about this step?
Thanks for your help,Leila
You'll need a registration that goes from the functional to the mni152. This has to be done in two steps, 1. Run mni152reg --s subject to create the anat-to-mni152 registration (needs FSL) 2. Run bbregister to get the anat-to-func reg (in lta format) 3. then combine them with mri_concatenate_lta, like mri_concatenate_lta $SUBJECTS/subject/mri/transforms/reg.mni152.2mm.lta bbr.lta output.lta Then use mri_vol2vol with --reg output.lta (and not --mni152reg)
On 6/15/16 5:55 AM, Leila Reddy wrote:
Hi,
I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in Freeview:
mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o mask_in_Native.nii --mni152reg
The overlay of the mask on f.nii in Freeview is mostly outside the brain.
How can I go about this step?
Thanks for your help, Leila
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, Thanks for your reply. When I run mni152reg I get an error : ERROR: Flag --lta unrecognized I'm using v 1.9 of this file.
I found a post that said to download a newer version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
but it doesn't seem to be there anymore.
Thanks, Leila
On Wednesday, June 15, 2016 11:55 AM, Leila Reddy leils@yahoo.com wrote:
Hi, I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in Freeview: mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o mask_in_Native.nii --mni152reg The overlay of the mask on f.nii in Freeview is mostly outside the brain.
How can I go about this step?
Thanks for your help,Leila
Try now
On 06/15/2016 06:30 PM, Leila Reddy wrote:
Hi Doug,
Thanks for your reply.
When I run mni152reg I get an error : ERROR: Flag --lta unrecognized
I'm using v 1.9 of this file.
I found a post that said to download a newer version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
but it doesn't seem to be there anymore.
Thanks, Leila
On Wednesday, June 15, 2016 11:55 AM, Leila Reddy leils@yahoo.com wrote:
Hi,
I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in Freeview:
mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o mask_in_Native.nii --mni152reg
The overlay of the mask on f.nii in Freeview is mostly outside the brain.
How can I go about this step?
Thanks for your help, Leila
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi FS Experts, I'm trying to use the mni152reg command but I get an error that --lta is not recognized. It appears that fslregister doesn't have this option. There was a previous post about this problemhttp://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41953.html but I can't figure out if the problem had been solved. The version of mni152reg I am using is$Id: mni152reg,v 1.9 2014/07/07 18:59:08 greve Exp $ on Mac OS 10.8.
Thanks,Leila
On Wednesday, June 15, 2016 11:55 AM, Leila Reddy leils@yahoo.com wrote:
Hi, I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in Freeview: mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o mask_in_Native.nii --mni152reg The overlay of the mask on f.nii in Freeview is mostly outside the brain.
How can I go about this step?
Thanks for your help,Leila
Is this problem resolved? There is a new version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
On 06/16/2016 11:05 AM, Leila Reddy wrote:
Hi FS Experts,
I'm trying to use the mni152reg command but I get an error that --lta is not recognized.
It appears that fslregister doesn't have this option. There was a previous post about this problem http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41953.html
but I can't figure out if the problem had been solved. The version of mni152reg I am using is $Id: mni152reg,v 1.9 2014/07/07 18:59:08 greve Exp $ on Mac OS 10.8.
Thanks, Leila
On Wednesday, June 15, 2016 11:55 AM, Leila Reddy leils@yahoo.com wrote:
Hi,
I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in Freeview:
mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o mask_in_Native.nii --mni152reg
The overlay of the mask on f.nii in Freeview is mostly outside the brain.
How can I go about this step?
Thanks for your help, Leila
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Leila Reddy