Hello Freesurfer Experts,
I was wondering if someone can help me understand which options I need to include with mri_vol2surf for the following situation?
I am trying to take group stats generated within FEAT that are in MNI152_2mm space and registrar/project those to fsaverage inflated surface.
When I tried a quick visualization using just tksurfer and overlaying my MNI space vol images, there seemed to be anatomical/registration differences between where each space displayed the stats.
I then attempted to use mri_vol2surf (command below) in hopes of better aligning these two spaces, but the statistical intensity values have been lost and I am not confident that this command worked in the way I thought it might/would like it to.
I am not sure which flags/options may be best in this situation, but any insight you may have is greatly appreciated!
Command used: mri_vol2surf --mov /.../tstat2.nii.gz --ref /.../MNI152_T1_2mm_brain.nii.gz --reg fsaverage --mni152reg --hemi rh --surf white --o /.../stats/
Is part of my problem that I have not specified a particular --out_type?
Terminal Output: srcvol = /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/tstat2.nii.gz srcreg = /usr/local/freesurfer/stable5_3_0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /space/sake/3/users/inverse/subjects/fsaverage/surf/rh.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 = 21216 Writing to /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/ Dim: 163842 1 1 non-standard value for imnr1 (1, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (163842, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure
Outputed files: COR-001 COR-.info
Command used for viewing:
tksurfer fsaverage rh white -overlay COR-001
Thank you for the help,
Jacob
The target has to be the freesurfer anatomical of the target subject (fsaverage in this case). You can get this by specifying --fstarg. The --reg is for the registration file; I'm surprised that the cmd actually ran. You just need to specify an output file with extension. Try the cmd below
mri_vol2surf --mov /.../tstat2.nii.gz --fstarg --mni152reg --hemi rh --surf white --o /.../stats/output.mgh
On 04/30/2014 11:55 AM, JacobML@nmr.mgh.harvard.edu wrote:
Hello Freesurfer Experts,
I was wondering if someone can help me understand which options I need to include with mri_vol2surf for the following situation?
I am trying to take group stats generated within FEAT that are in MNI152_2mm space and registrar/project those to fsaverage inflated surface.
When I tried a quick visualization using just tksurfer and overlaying my MNI space vol images, there seemed to be anatomical/registration differences between where each space displayed the stats.
I then attempted to use mri_vol2surf (command below) in hopes of better aligning these two spaces, but the statistical intensity values have been lost and I am not confident that this command worked in the way I thought it might/would like it to.
I am not sure which flags/options may be best in this situation, but any insight you may have is greatly appreciated!
Command used: mri_vol2surf --mov /.../tstat2.nii.gz --ref /.../MNI152_T1_2mm_brain.nii.gz --reg fsaverage --mni152reg --hemi rh --surf white --o /.../stats/
Is part of my problem that I have not specified a particular --out_type?
Terminal Output: srcvol = /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/tstat2.nii.gz srcreg = /usr/local/freesurfer/stable5_3_0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /space/sake/3/users/inverse/subjects/fsaverage/surf/rh.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 = 21216 Writing to /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/ Dim: 163842 1 1 non-standard value for imnr1 (1, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (163842, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure
Outputed files: COR-001 COR-.info
Command used for viewing:
tksurfer fsaverage rh white -overlay COR-001
Thank you for the help,
Jacob
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Doug,
Thank you for such a quick reply and for your insight.
I have adjusted the cmd but --fstarg seems to not be recognized as an option ("ERROR: Option --fstarg unknown").
I also tried to include fsaverage following --fstarg, but I still received the same error.
I am using stable53 and the usage of mri_vol2surf does not seem to include --fstarg. Will using "--trgsubject fsaverage" instead of "--fstarg " accomplish the goal of setting fsaverage as the target, or are there additional details that I may be overlooking?
Please let me know what you think best!
Thank you,
Jacob
The target has to be the freesurfer anatomical of the target subject (fsaverage in this case). You can get this by specifying --fstarg. The --reg is for the registration file; I'm surprised that the cmd actually ran. You just need to specify an output file with extension. Try the cmd below
mri_vol2surf --mov /.../tstat2.nii.gz --fstarg --mni152reg --hemi rh --surf white --o /.../stats/output.mgh
On 04/30/2014 11:55 AM, JacobML@nmr.mgh.harvard.edu wrote:
Hello Freesurfer Experts,
I was wondering if someone can help me understand which options I need to include with mri_vol2surf for the following situation?
I am trying to take group stats generated within FEAT that are in MNI152_2mm space and registrar/project those to fsaverage inflated surface.
When I tried a quick visualization using just tksurfer and overlaying my MNI space vol images, there seemed to be anatomical/registration differences between where each space displayed the stats.
I then attempted to use mri_vol2surf (command below) in hopes of better aligning these two spaces, but the statistical intensity values have been lost and I am not confident that this command worked in the way I thought it might/would like it to.
I am not sure which flags/options may be best in this situation, but any insight you may have is greatly appreciated!
Command used: mri_vol2surf --mov /.../tstat2.nii.gz --ref /.../MNI152_T1_2mm_brain.nii.gz --reg fsaverage --mni152reg --hemi rh --surf white --o /.../stats/
Is part of my problem that I have not specified a particular --out_type?
Terminal Output: srcvol = /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/tstat2.nii.gz srcreg = /usr/local/freesurfer/stable5_3_0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /space/sake/3/users/inverse/subjects/fsaverage/surf/rh.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 = 21216 Writing to /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/ Dim: 163842 1 1 non-standard value for imnr1 (1, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (163842, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure
Outputed files: COR-001 COR-.info
Command used for viewing:
tksurfer fsaverage rh white -overlay COR-001
Thank you for the help,
Jacob
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
oops, sorry, that is an option to mri_vol2vol, not vol2surf. Just exclude that option
On 04/30/2014 02:48 PM, JacobML@nmr.mgh.harvard.edu wrote:
Hello Doug,
Thank you for such a quick reply and for your insight.
I have adjusted the cmd but --fstarg seems to not be recognized as an option ("ERROR: Option --fstarg unknown").
I also tried to include fsaverage following --fstarg, but I still received the same error.
I am using stable53 and the usage of mri_vol2surf does not seem to include --fstarg. Will using "--trgsubject fsaverage" instead of "--fstarg " accomplish the goal of setting fsaverage as the target, or are there additional details that I may be overlooking?
Please let me know what you think best!
Thank you,
Jacob
The target has to be the freesurfer anatomical of the target subject (fsaverage in this case). You can get this by specifying --fstarg. The --reg is for the registration file; I'm surprised that the cmd actually ran. You just need to specify an output file with extension. Try the cmd below
mri_vol2surf --mov /.../tstat2.nii.gz --fstarg --mni152reg --hemi rh --surf white --o /.../stats/output.mgh
On 04/30/2014 11:55 AM, JacobML@nmr.mgh.harvard.edu wrote:
Hello Freesurfer Experts,
I was wondering if someone can help me understand which options I need to include with mri_vol2surf for the following situation?
I am trying to take group stats generated within FEAT that are in MNI152_2mm space and registrar/project those to fsaverage inflated surface.
When I tried a quick visualization using just tksurfer and overlaying my MNI space vol images, there seemed to be anatomical/registration differences between where each space displayed the stats.
I then attempted to use mri_vol2surf (command below) in hopes of better aligning these two spaces, but the statistical intensity values have been lost and I am not confident that this command worked in the way I thought it might/would like it to.
I am not sure which flags/options may be best in this situation, but any insight you may have is greatly appreciated!
Command used: mri_vol2surf --mov /.../tstat2.nii.gz --ref /.../MNI152_T1_2mm_brain.nii.gz --reg fsaverage --mni152reg --hemi rh --surf white --o /.../stats/
Is part of my problem that I have not specified a particular --out_type?
Terminal Output: srcvol = /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/tstat2.nii.gz srcreg = /usr/local/freesurfer/stable5_3_0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /space/sake/3/users/inverse/subjects/fsaverage/surf/rh.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 = 21216 Writing to /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/ Dim: 163842 1 1 non-standard value for imnr1 (1, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (163842, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure
Outputed files: COR-001 COR-.info
Command used for viewing:
tksurfer fsaverage rh white -overlay COR-001
Thank you for the help,
Jacob
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
No worries, thank you for the help!
oops, sorry, that is an option to mri_vol2vol, not vol2surf. Just exclude that option
On 04/30/2014 02:48 PM, JacobML@nmr.mgh.harvard.edu wrote:
Hello Doug,
Thank you for such a quick reply and for your insight.
I have adjusted the cmd but --fstarg seems to not be recognized as an option ("ERROR: Option --fstarg unknown").
I also tried to include fsaverage following --fstarg, but I still received the same error.
I am using stable53 and the usage of mri_vol2surf does not seem to include --fstarg. Will using "--trgsubject fsaverage" instead of "--fstarg " accomplish the goal of setting fsaverage as the target, or are there additional details that I may be overlooking?
Please let me know what you think best!
Thank you,
Jacob
The target has to be the freesurfer anatomical of the target subject (fsaverage in this case). You can get this by specifying --fstarg. The --reg is for the registration file; I'm surprised that the cmd actually ran. You just need to specify an output file with extension. Try the cmd below
mri_vol2surf --mov /.../tstat2.nii.gz --fstarg --mni152reg --hemi rh --surf white --o /.../stats/output.mgh
On 04/30/2014 11:55 AM, JacobML@nmr.mgh.harvard.edu wrote:
Hello Freesurfer Experts,
I was wondering if someone can help me understand which options I need to include with mri_vol2surf for the following situation?
I am trying to take group stats generated within FEAT that are in MNI152_2mm space and registrar/project those to fsaverage inflated surface.
When I tried a quick visualization using just tksurfer and overlaying my MNI space vol images, there seemed to be anatomical/registration differences between where each space displayed the stats.
I then attempted to use mri_vol2surf (command below) in hopes of better aligning these two spaces, but the statistical intensity values have been lost and I am not confident that this command worked in the way I thought it might/would like it to.
I am not sure which flags/options may be best in this situation, but any insight you may have is greatly appreciated!
Command used: mri_vol2surf --mov /.../tstat2.nii.gz --ref /.../MNI152_T1_2mm_brain.nii.gz --reg fsaverage --mni152reg --hemi rh --surf white --o /.../stats/
Is part of my problem that I have not specified a particular --out_type?
Terminal Output: srcvol = /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/tstat2.nii.gz srcreg = /usr/local/freesurfer/stable5_3_0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /space/sake/3/users/inverse/subjects/fsaverage/surf/rh.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 = 21216 Writing to /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/ Dim: 163842 1 1 non-standard value for imnr1 (1, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (163842, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure
Outputed files: COR-001 COR-.info
Command used for viewing:
tksurfer fsaverage rh white -overlay COR-001
Thank you for the help,
Jacob
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
JacobML＠nmr.mgh.harvard.edu