Dear Freesurfer community,
I have processed a subject (name:P061_pre, 3D MPRAGE T1) with Freesurfer 5.1. A resection area has been defiened on this volume and exists as a binary volume (1:voxels of interest, 0:others) lesionMask.mgz. I now would like to project this volume on the surface of the subject, e.g. lh.white. I have tried using mri_vol2surf : mri_vol2surf --src lesionMask.mgz --out lesionMask_surf.mgh --out_type mgh --hemi lh --regheader P061_pre
The command seems to work:
srcvol = lesionMask.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /root/data/FS51/freesurfer/subjects/P061_pre/mri/orig.mgz as target reference. Reading surface /root/data/FS51/freesurfer/subjects/P061_pre/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 79054 Writing to ./lesionMask_surf.mgh Dim: 128233 1 1
But when trying to open the surface with freeview, it returns an error message : freeview -f lesionMask_surf.mgh ERROR: MRISread: cannot read surface data from file /home/epilepsy/sorted/P061/preMR/lesionMask_surf.mgh!
Segmentation fault
What did I miss ?
Thanks for your help,
The output of mri_vol2surf is not a surface but an overlay on a surface. You will need to run something like:
freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh
You'll need to set the threshold to 0.5 in order to see the mask. doug
On 03/07/2013 05:53 AM, Christopher wrote:
Dear Freesurfer community,
I have processed a subject (name:P061_pre, 3D MPRAGE T1) with Freesurfer 5.1. A resection area has been defiened on this volume and exists as a binary volume (1:voxels of interest, 0:others) lesionMask.mgz. I now would like to project this volume on the surface of the subject, e.g. lh.white. I have tried using mri_vol2surf : mri_vol2surf --src lesionMask.mgz --out lesionMask_surf.mgh --out_type mgh --hemi lh --regheader P061_pre
The command seems to work:
srcvol = lesionMask.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /root/data/FS51/freesurfer/subjects/P061_pre/mri/orig.mgz as target reference. Reading surface /root/data/FS51/freesurfer/subjects/P061_pre/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 79054 Writing to ./lesionMask_surf.mgh Dim: 128233 1 1
But when trying to open the surface with freeview, it returns an error message : freeview -f lesionMask_surf.mgh ERROR: MRISread: cannot read surface data from file /home/epilepsy/sorted/P061/preMR/lesionMask_surf.mgh!
Segmentation fault
What did I miss ?
Thanks for your help,
Thanks Doug. I can know visualize the resected area using freeview.
As the output of mri_vol2surf produces an overlay and not a surface, measurements of area or/and intersection with other outputs from mri_vol2surf are not possible using mris_* functions. What is the best strategy to follow to be able to do simple measurments on these mri_vol2surf outputs ? Transform to surface, but how ?
Thanks in advance,
Christopher
The output of mri_vol2surf is not a surface but an overlay on a surface. You will need to run something like:
freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh
You'll need to set the threshold to 0.5 in order to see the mask. doug
Hi Christopher, I'm not sure I understand your question. What do you mean by "simple measurements"? doug
On 3/11/13 10:59 AM, Christopher wrote:
Thanks Doug. I can know visualize the resected area using freeview.
As the output of mri_vol2surf produces an overlay and not a surface, measurements of area or/and intersection with other outputs from mri_vol2surf are not possible using mris_* functions. What is the best strategy to follow to be able to do simple measurments on these mri_vol2surf outputs ? Transform to surface, but how ?
Thanks in advance,
Christopher
The output of mri_vol2surf is not a surface but an overlay on a surface. You will need to run something like:
freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh
You'll need to set the threshold to 0.5 in order to see the mask. doug
Hi Doug,
Not really clear, I do agree. 1/ I would like to measure the area of the surface called lesionMask_surf.mgh obtained with mri_vol2surf. 2/ In addition, I have two methods (M1 and M2) to measure a resected volume. The binary volumes M1_vol and M2_vol are processed with mri_vol2surf to obtain M1_surf and M2_surf. I would like to measure the area common to M1_surf and M2_surf.
Best,
Christopher
On 11.03.2013 18:12, Douglas Greve wrote:
Hi Christopher, I'm not sure I understand your question. What do you mean by "simple measurements"? doug
On 3/11/13 10:59 AM, Christopher wrote:
Thanks Doug. I can know visualize the resected area using freeview.
As the output of mri_vol2surf produces an overlay and not a surface, measurements of area or/and intersection with other outputs from mri_vol2surf are not possible using mris_* functions. What is the best strategy to follow to be able to do simple measurments on these mri_vol2surf outputs ? Transform to surface, but how ?
Thanks in advance,
Christopher
The output of mri_vol2surf is not a surface but an overlay on a surface. You will need to run something like:
freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh
You'll need to set the threshold to 0.5 in order to see the mask. doug
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.
On 3/12/13 10:12 AM, Christopher wrote:
Hi Doug,
Not really clear, I do agree. 1/ I would like to measure the area of the surface called lesionMask_surf.mgh obtained with mri_vol2surf.
You can use mri_segstats, something like mri_segstats --i $SUBJECTS_DIR/$subject/surf/lh.area --seg lesionMask_surf.mgh --id 1 --accumulate --sum sum.dat The output is sum.dat. The number you will want will be the "Mean" column (column 6). Ignore the other columns that say NVoxels and Volume_mm3.
2/ In addition, I have two methods (M1 and M2) to measure a resected volume. The binary volumes M1_vol and M2_vol are processed with mri_vol2surf to obtain M1_surf and M2_surf. I would like to measure the area common to M1_surf and M2_surf.
First create a new volume corresponding to the overlap between the two: fscalc M1_surf.mgh and M2_surf.mgh -o M1_and_M2_surf.mgh Then use the command above to get the area doug
Best,
Christopher
On 11.03.2013 18:12, Douglas Greve wrote:
Hi Christopher, I'm not sure I understand your question. What do you mean by "simple measurements"? doug
On 3/11/13 10:59 AM, Christopher wrote:
Thanks Doug. I can know visualize the resected area using freeview.
As the output of mri_vol2surf produces an overlay and not a surface, measurements of area or/and intersection with other outputs from mri_vol2surf are not possible using mris_* functions. What is the best strategy to follow to be able to do simple measurments on these mri_vol2surf outputs ? Transform to surface, but how ?
Thanks in advance,
Christopher
The output of mri_vol2surf is not a surface but an overlay on a surface. You will need to run something like:
freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh
You'll need to set the threshold to 0.5 in order to see the mask. doug
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
-
Christopher -
Douglas Greve -
Douglas N Greve