Dear all, Any help that you could give on this pretty basic question would be much appreciated. I've been trying to use the excellent fmri-to-anatomical registration produced by Freesurfer's bbregister to convert a 4d volume time series to a GIFTI surface time series. So far, I have tried using mri_vol2surf and mris_convert as below, with no success. In this example, the dataset volume_time_series.nii is of size 64x64x37x96, where 96 is the number of time points. I would really appreciate it if anyone spots and would correct the usage error(s) that I must have made. ?? Thank you, Kathleen
mri_vol2surf --mov volume_time_series.nii --reg good_registration.dat --hemi lh --o surface_time_series_lh.mgh --projfrac 0.5 --interp nearest srcvol = volume_time_series.nii srcreg = good_registration.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.white Done reading source surface Reading thickness /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 Done mapping volume to surface Number of source voxels hit = 11133 Reshaping 19 (nvertices = 137275) Writing to surface_time_series_lh.mgh Dim: 7225 1 19
mris_convert surface_time_series_lh.mgh surface_time_series_lh.gii ERROR: MRISread: file 'surface_time_series_lh.mgh' has 0 vertices!
to convert time-series to gifti, use:
mris_convert -f ./surface_time_series_lh.mgh \ lh.white \ ./surface_time_series_lh.gii
notice usage of -f flag (see --help) and also a surface must be specified (this example uses the white surface)
also, i'd make sure that your file 'surface_time_series_lh.mgh' is valid (by viewing on surface or using mri_info to look at dimensions).
n.
On Thu, 2010-09-16 at 12:49 -0400, Hansen, Kathleen (NIH/NIMH) [F] wrote:
Dear all, Any help that you could give on this pretty basic question would be much appreciated. I've been trying to use the excellent fmri-to-anatomical registration produced by Freesurfer's bbregister to convert a 4d volume time series to a GIFTI surface time series. So far, I have tried using mri_vol2surf and mris_convert as below, with no success. In this example, the dataset volume_time_series.nii is of size 64x64x37x96, where 96 is the number of time points. I would really appreciate it if anyone spots and would correct the usage error(s) that I must have made. ?? Thank you, Kathleen
mri_vol2surf --mov volume_time_series.nii --reg good_registration.dat --hemi lh --o surface_time_series_lh.mgh --projfrac 0.5 --interp nearest srcvol = volume_time_series.nii srcreg = good_registration.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.white Done reading source surface Reading thickness /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 Done mapping volume to surface Number of source voxels hit = 11133 Reshaping 19 (nvertices = 137275) Writing to surface_time_series_lh.mgh Dim: 7225 1 19
mris_convert surface_time_series_lh.mgh surface_time_series_lh.gii ERROR: MRISread: file 'surface_time_series_lh.mgh' has 0 vertices!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks so much, Nick. I used your suggestion for the call to mris_convert and it seems to be working fine. Thanks also for the pointer to mri_info to check dimensions. This gave more helpful info than the output message from my original mri_vol2surf call, which reported the first 3 but not the 4th dimension. With the mri_info output it became obvious that --noreshape was needed in the mri_vol2surf call. I really appreciate it. -Kathleen
On 9/16/10 2:23 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
to convert time-series to gifti, use:
mris_convert -f ./surface_time_series_lh.mgh \ lh.white \ ./surface_time_series_lh.gii
notice usage of -f flag (see --help) and also a surface must be specified (this example uses the white surface)
also, i'd make sure that your file 'surface_time_series_lh.mgh' is valid (by viewing on surface or using mri_info to look at dimensions).
n.
On Thu, 2010-09-16 at 12:49 -0400, Hansen, Kathleen (NIH/NIMH) [F] wrote:
Dear all, Any help that you could give on this pretty basic question would be much appreciated. I've been trying to use the excellent fmri-to-anatomical registration produced by Freesurfer's bbregister to convert a 4d volume time series to a GIFTI surface time series. So far, I have tried using mri_vol2surf and mris_convert as below, with no success. In this example, the dataset volume_time_series.nii is of size 64x64x37x96, where 96 is the number of time points. I would really appreciate it if anyone spots and would correct the usage error(s) that I must have made. ?? Thank you, Kathleen
mri_vol2surf --mov volume_time_series.nii --reg good_registration.dat --hemi lh --o surface_time_series_lh.mgh --projfrac 0.5 --interp nearest srcvol = volume_time_series.nii srcreg = good_registration.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.white Done reading source surface Reading thickness /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 Done mapping volume to surface Number of source voxels hit = 11133 Reshaping 19 (nvertices = 137275) Writing to surface_time_series_lh.mgh Dim: 7225 1 19
mris_convert surface_time_series_lh.mgh surface_time_series_lh.gii ERROR: MRISread: file 'surface_time_series_lh.mgh' has 0 vertices!
Freesurfer mailing list 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.
Sorry, Nick, a followup question. After performing mris_convert on two time series files as below, I noticed something odd about file size and wonder if there is a problem. The input .mgh time series files were the same size as seen by an ls -l command, 52525379. But the output file for one .gii time series was 13969434 and the output file for the other .gii time series was 13920322. So the two outputs are not only smaller but also different sizes. A call to mri_info does confirm that both output files have the expected dimensions (vertices x time points). Is the file size a concern? Thanks, Kathleen
On 9/16/10 2:37 PM, "Hansen, Kathleen (NIH/NIMH) [F]" hansenka@mail.nih.gov wrote:
Thanks so much, Nick. I used your suggestion for the call to mris_convert and it seems to be working fine. Thanks also for the pointer to mri_info to check dimensions. This gave more helpful info than the output message from my original mri_vol2surf call, which reported the first 3 but not the 4th dimension. With the mri_info output it became obvious that --noreshape was needed in the mri_vol2surf call. I really appreciate it. -Kathleen
On 9/16/10 2:23 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
to convert time-series to gifti, use:
mris_convert -f ./surface_time_series_lh.mgh \ lh.white \ ./surface_time_series_lh.gii
notice usage of -f flag (see --help) and also a surface must be specified (this example uses the white surface)
also, i'd make sure that your file 'surface_time_series_lh.mgh' is valid (by viewing on surface or using mri_info to look at dimensions).
n.
On Thu, 2010-09-16 at 12:49 -0400, Hansen, Kathleen (NIH/NIMH) [F] wrote:
Dear all, Any help that you could give on this pretty basic question would be much appreciated. I've been trying to use the excellent fmri-to-anatomical registration produced by Freesurfer's bbregister to convert a 4d volume time series to a GIFTI surface time series. So far, I have tried using mri_vol2surf and mris_convert as below, with no success. In this example, the dataset volume_time_series.nii is of size 64x64x37x96, where 96 is the number of time points. I would really appreciate it if anyone spots and would correct the usage error(s) that I must have made. ?? Thank you, Kathleen
mri_vol2surf --mov volume_time_series.nii --reg good_registration.dat --hemi lh --o surface_time_series_lh.mgh --projfrac 0.5 --interp nearest srcvol = volume_time_series.nii srcreg = good_registration.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.white Done reading source surface Reading thickness /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 Done mapping volume to surface Number of source voxels hit = 11133 Reshaping 19 (nvertices = 137275) Writing to surface_time_series_lh.mgh Dim: 7225 1 19
mris_convert surface_time_series_lh.mgh surface_time_series_lh.gii ERROR: MRISread: file 'surface_time_series_lh.mgh' has 0 vertices!
Freesurfer mailing list 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.
that should be fine. the .gii file is compressed, whereas the .mgh file is not.
n.
On Mon, 2010-09-20 at 11:28 -0400, Hansen, Kathleen (NIH/NIMH) [F] wrote:
Sorry, Nick, a followup question. After performing mris_convert on two time series files as below, I noticed something odd about file size and wonder if there is a problem. The input .mgh time series files were the same size as seen by an ls -l command, 52525379. But the output file for one .gii time series was 13969434 and the output file for the other .gii time series was 13920322. So the two outputs are not only smaller but also different sizes. A call to mri_info does confirm that both output files have the expected dimensions (vertices x time points). Is the file size a concern? Thanks, Kathleen
On 9/16/10 2:37 PM, "Hansen, Kathleen (NIH/NIMH) [F]" hansenka@mail.nih.gov wrote:
Thanks so much, Nick. I used your suggestion for the call to mris_convert and it seems to be working fine. Thanks also for the pointer to mri_info to check dimensions. This gave more helpful info than the output message from my original mri_vol2surf call, which reported the first 3 but not the 4th dimension. With the mri_info output it became obvious that --noreshape was needed in the mri_vol2surf call. I really appreciate it. -Kathleen
On 9/16/10 2:23 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
to convert time-series to gifti, use:
mris_convert -f ./surface_time_series_lh.mgh \ lh.white \ ./surface_time_series_lh.gii
notice usage of -f flag (see --help) and also a surface must be specified (this example uses the white surface)
also, i'd make sure that your file 'surface_time_series_lh.mgh' is valid (by viewing on surface or using mri_info to look at dimensions).
n.
On Thu, 2010-09-16 at 12:49 -0400, Hansen, Kathleen (NIH/NIMH) [F] wrote:
Dear all, Any help that you could give on this pretty basic question would be much appreciated. I've been trying to use the excellent fmri-to-anatomical registration produced by Freesurfer's bbregister to convert a 4d volume time series to a GIFTI surface time series. So far, I have tried using mri_vol2surf and mris_convert as below, with no success. In this example, the dataset volume_time_series.nii is of size 64x64x37x96, where 96 is the number of time points. I would really appreciate it if anyone spots and would correct the usage error(s) that I must have made. ?? Thank you, Kathleen
mri_vol2surf --mov volume_time_series.nii --reg good_registration.dat --hemi lh --o surface_time_series_lh.mgh --projfrac 0.5 --interp nearest srcvol = volume_time_series.nii srcreg = good_registration.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.white Done reading source surface Reading thickness /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 Done mapping volume to surface Number of source voxels hit = 11133 Reshaping 19 (nvertices = 137275) Writing to surface_time_series_lh.mgh Dim: 7225 1 19
mris_convert surface_time_series_lh.mgh surface_time_series_lh.gii ERROR: MRISread: file 'surface_time_series_lh.mgh' has 0 vertices!
Freesurfer mailing list 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.
freesurfer@nmr.mgh.harvard.edu
-
Hansen, Kathleen (NIH/NIMH) [F] -
Nick Schmansky