Hi there,
I am trying to interpolate a volume of tstats to the average surface with mri_vol2surf but I am getting the error below. Does mri_vol2surf take all the inputs that mri_convert takes? Is this a float2int problem mentioned in the bugs section of the --help? If the latter, what argument should I specify with --float2int? Thanks in advance for your time.
Cheers,
-Morgan
mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average --hemi lh --surf inflated --surfreg lh.sphere.reg --out lh.vbm_surf_results.mgh --srcreg reg.dat srcvol = vbm_results_mni305_tl.nii.gz srcreg = reg.dat srcregold = 0 srcwarp unspecified surf = inflated hemi = lh trgsubject = average surfreg = lh.sphere.reg interp = nearest float2int = round INFO: float2int code = 2 niiRead(): error opening file /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24
Morgan,
I'm not so sure this is a float2int problem (but Doug may be able to answer when he gets back next week). Can you read that .nii.gz file with mri_info? Can you convert it to, say, an .mgz file using mri_convert? The error message looks like it can't interpret the file as a NIFTI file (the preceeding float2int message being misleading in this instance, I think).
Nick
On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote:
Hi there,
I am trying to interpolate a volume of tstats to the average surface with mri_vol2surf but I am getting the error below. Does mri_vol2surf take all the inputs that mri_convert takes? Is this a float2int problem mentioned in the bugs section of the --help? If the latter, what argument should I specify with --float2int? Thanks in advance for your time.
Cheers,
-Morgan
mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average --hemi lh --surf inflated --surfreg lh.sphere.reg --out lh.vbm_surf_results.mgh --srcreg reg.dat srcvol = vbm_results_mni305_tl.nii.gz srcreg = reg.dat srcregold = 0 srcwarp unspecified surf = inflated hemi = lh trgsubject = average surfreg = lh.sphere.reg interp = nearest float2int = round INFO: float2int code = 2 niiRead(): error opening file /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
The file looks fine in mri_info and it is convertible to mgz. If I convert it to Analyze (which I can view using fslview) the mri_vol2surf command works. Happy to send the files along if they would be helpful.
I was trying to get a rough approximation of MNI152 space group results projected onto the average surface by registering the volumetric group results with FS's mni305 template and using an identity reg.dat as the srcreg. I have done this but the results look wrong. I have checked the registration of the group results to the mni305 template. Is there anything else I could check? Should I be doing this differently?
Cheers,
-Morgan
Nick Schmansky wrote:
Morgan,
I'm not so sure this is a float2int problem (but Doug may be able to answer when he gets back next week). Can you read that .nii.gz file with mri_info? Can you convert it to, say, an .mgz file using mri_convert? The error message looks like it can't interpret the file as a NIFTI file (the preceeding float2int message being misleading in this instance, I think).
Nick
On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote:
Hi there,
I am trying to interpolate a volume of tstats to the average surface with mri_vol2surf but I am getting the error below. Does mri_vol2surf take all the inputs that mri_convert takes? Is this a float2int problem mentioned in the bugs section of the --help? If the latter, what argument should I specify with --float2int? Thanks in advance for your time.
Cheers,
-Morgan
mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average --hemi lh --surf inflated --surfreg lh.sphere.reg --out lh.vbm_surf_results.mgh --srcreg reg.dat srcvol = vbm_results_mni305_tl.nii.gz srcreg = reg.dat srcregold = 0 srcwarp unspecified surf = inflated hemi = lh trgsubject = average surfreg = lh.sphere.reg interp = nearest float2int = round INFO: float2int code = 2 niiRead(): error opening file /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Morgan Hough wrote:
Hi Nick,
The file looks fine in mri_info and it is convertible to mgz. If I convert it to Analyze (which I can view using fslview) the mri_vol2surf command works. Happy to send the files along if they would be helpful.
Hmmm, that's strange. It's not a float2int issue. It's having problems opening that file. It is strange because it uses exactly the same code that mri_info and mri_convert use to open it. Is is possible that you have mixed versions? Maybe the vol2surf version you have is older?
I was trying to get a rough approximation of MNI152 space group results projected onto the average surface by registering the volumetric group results with FS's mni305 template and using an identity reg.dat as the srcreg. I have done this but the results look wrong. I have checked the registration of the group results to the mni305 template. Is there anything else I could check? Should I be doing this differently?
That sounds correct. If the reg looks ok, then you can load your t map onto fsaverage in tkmedit along with the surfaces and see whether they intersect your activation.
doug
Cheers,
-Morgan
Nick Schmansky wrote:
Morgan,
I'm not so sure this is a float2int problem (but Doug may be able to answer when he gets back next week). Can you read that .nii.gz file with mri_info? Can you convert it to, say, an .mgz file using mri_convert? The error message looks like it can't interpret the file as a NIFTI file (the preceeding float2int message being misleading in this instance, I think).
Nick
On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote:
Hi there,
I am trying to interpolate a volume of tstats to the average surface with mri_vol2surf but I am getting the error below. Does mri_vol2surf take all the inputs that mri_convert takes? Is this a float2int problem mentioned in the bugs section of the --help? If the latter, what argument should I specify with --float2int? Thanks in advance for your time.
Cheers,
-Morgan
mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average --hemi lh --surf inflated --surfreg lh.sphere.reg --out lh.vbm_surf_results.mgh --srcreg reg.dat srcvol = vbm_results_mni305_tl.nii.gz srcreg = reg.dat srcregold = 0 srcwarp unspecified surf = inflated hemi = lh trgsubject = average surfreg = lh.sphere.reg interp = nearest float2int = round INFO: float2int code = 2 niiRead(): error opening file /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz
ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24 _______________________________________________ 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
Hi Doug,
Multiple versions are always a concern since we have multiple platforms but I have checked them all and I get
$Id: mri_vol2surf.c,v 1.26 2006/02/09 16:31:29 greve Exp $
on all platforms.
I think my problems with the actual output now are due to the problems of trying to project MNI group results onto the average surface - sometimes the results fall between the average surfaces. When viewed in tkmedit you can see why it is not mapping all the MNI group results to the surface. Do you think any projection distance changes would make sense to get a rough approx. of what the t-stats are closest to in this case?
Cheers,
-Morgan
Doug Greve wrote:
Morgan Hough wrote:
Hi Nick,
The file looks fine in mri_info and it is convertible to mgz. If I convert it to Analyze (which I can view using fslview) the mri_vol2surf command works. Happy to send the files along if they would be helpful.
Hmmm, that's strange. It's not a float2int issue. It's having problems opening that file. It is strange because it uses exactly the same code that mri_info and mri_convert use to open it. Is is possible that you have mixed versions? Maybe the vol2surf version you have is older?
I was trying to get a rough approximation of MNI152 space group results projected onto the average surface by registering the volumetric group results with FS's mni305 template and using an identity reg.dat as the srcreg. I have done this but the results look wrong. I have checked the registration of the group results to the mni305 template. Is there anything else I could check? Should I be doing this differently?
That sounds correct. If the reg looks ok, then you can load your t map onto fsaverage in tkmedit along with the surfaces and see whether they intersect your activation.
doug
Cheers,
-Morgan
Nick Schmansky wrote:
Morgan,
I'm not so sure this is a float2int problem (but Doug may be able to answer when he gets back next week). Can you read that .nii.gz file with mri_info? Can you convert it to, say, an .mgz file using mri_convert? The error message looks like it can't interpret the file as a NIFTI file (the preceeding float2int message being misleading in this instance, I think).
Nick
On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote:
Hi there,
I am trying to interpolate a volume of tstats to the average surface with mri_vol2surf but I am getting the error below. Does mri_vol2surf take all the inputs that mri_convert takes? Is this a float2int problem mentioned in the bugs section of the --help? If the latter, what argument should I specify with --float2int? Thanks in advance for your time.
Cheers,
-Morgan
mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average --hemi lh --surf inflated --surfreg lh.sphere.reg --out lh.vbm_surf_results.mgh --srcreg reg.dat srcvol = vbm_results_mni305_tl.nii.gz srcreg = reg.dat srcregold = 0 srcwarp unspecified surf = inflated hemi = lh trgsubject = average surfreg = lh.sphere.reg interp = nearest float2int = round INFO: float2int code = 2 niiRead(): error opening file /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz
ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24 _______________________________________________ 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
What do you mean by "between the average surfaces"? Between the white and pial? There are various projection options, eg, you can average between them or take the max. This type of comparison is always a bit ill-posed because the surface in a 3d talairach imbedding space is not that meaningful. You might try mapping your surface-based results into the talairach volume.
doug
Morgan Hough wrote:
Hi Doug,
Multiple versions are always a concern since we have multiple platforms but I have checked them all and I get
$Id: mri_vol2surf.c,v 1.26 2006/02/09 16:31:29 greve Exp $
on all platforms.
I think my problems with the actual output now are due to the problems of trying to project MNI group results onto the average surface - sometimes the results fall between the average surfaces. When viewed in tkmedit you can see why it is not mapping all the MNI group results to the surface. Do you think any projection distance changes would make sense to get a rough approx. of what the t-stats are closest to in this case?
Cheers,
-Morgan
Doug Greve wrote:
Morgan Hough wrote:
Hi Nick,
The file looks fine in mri_info and it is convertible to mgz. If I convert it to Analyze (which I can view using fslview) the mri_vol2surf command works. Happy to send the files along if they would be helpful.
Hmmm, that's strange. It's not a float2int issue. It's having problems opening that file. It is strange because it uses exactly the same code that mri_info and mri_convert use to open it. Is is possible that you have mixed versions? Maybe the vol2surf version you have is older?
I was trying to get a rough approximation of MNI152 space group results projected onto the average surface by registering the volumetric group results with FS's mni305 template and using an identity reg.dat as the srcreg. I have done this but the results look wrong. I have checked the registration of the group results to the mni305 template. Is there anything else I could check? Should I be doing this differently?
That sounds correct. If the reg looks ok, then you can load your t map onto fsaverage in tkmedit along with the surfaces and see whether they intersect your activation.
doug
Cheers,
-Morgan
Nick Schmansky wrote:
Morgan,
I'm not so sure this is a float2int problem (but Doug may be able to answer when he gets back next week). Can you read that .nii.gz file with mri_info? Can you convert it to, say, an .mgz file using mri_convert? The error message looks like it can't interpret the file as a NIFTI file (the preceeding float2int message being misleading in this instance, I think).
Nick
On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote:
Hi there,
I am trying to interpolate a volume of tstats to the average surface with mri_vol2surf but I am getting the error below. Does mri_vol2surf take all the inputs that mri_convert takes? Is this a float2int problem mentioned in the bugs section of the --help? If the latter, what argument should I specify with --float2int? Thanks in advance for your time.
Cheers,
-Morgan
mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average --hemi lh --surf inflated --surfreg lh.sphere.reg --out lh.vbm_surf_results.mgh --srcreg reg.dat srcvol = vbm_results_mni305_tl.nii.gz srcreg = reg.dat srcregold = 0 srcwarp unspecified surf = inflated hemi = lh trgsubject = average surfreg = lh.sphere.reg interp = nearest float2int = round INFO: float2int code = 2 niiRead(): error opening file /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz
ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24 _______________________________________________ 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
Hey Doug,
Sorry, what I meant was between the left and right surfaces like in the image that I attached.
Cheers,
-Morgan
Doug Greve wrote:
What do you mean by "between the average surfaces"? Between the white and pial? There are various projection options, eg, you can average between them or take the max. This type of comparison is always a bit ill-posed because the surface in a 3d talairach imbedding space is not that meaningful. You might try mapping your surface-based results into the talairach volume.
doug
Morgan Hough wrote:
Hi Doug,
Multiple versions are always a concern since we have multiple platforms but I have checked them all and I get
$Id: mri_vol2surf.c,v 1.26 2006/02/09 16:31:29 greve Exp $
on all platforms.
I think my problems with the actual output now are due to the problems of trying to project MNI group results onto the average surface - sometimes the results fall between the average surfaces. When viewed in tkmedit you can see why it is not mapping all the MNI group results to the surface. Do you think any projection distance changes would make sense to get a rough approx. of what the t-stats are closest to in this case?
Cheers,
-Morgan
Doug Greve wrote:
Morgan Hough wrote:
Hi Nick,
The file looks fine in mri_info and it is convertible to mgz. If I convert it to Analyze (which I can view using fslview) the mri_vol2surf command works. Happy to send the files along if they would be helpful.
Hmmm, that's strange. It's not a float2int issue. It's having problems opening that file. It is strange because it uses exactly the same code that mri_info and mri_convert use to open it. Is is possible that you have mixed versions? Maybe the vol2surf version you have is older?
I was trying to get a rough approximation of MNI152 space group results projected onto the average surface by registering the volumetric group results with FS's mni305 template and using an identity reg.dat as the srcreg. I have done this but the results look wrong. I have checked the registration of the group results to the mni305 template. Is there anything else I could check? Should I be doing this differently?
That sounds correct. If the reg looks ok, then you can load your t map onto fsaverage in tkmedit along with the surfaces and see whether they intersect your activation.
doug
Cheers,
-Morgan
Nick Schmansky wrote:
Morgan,
I'm not so sure this is a float2int problem (but Doug may be able to answer when he gets back next week). Can you read that .nii.gz file with mri_info? Can you convert it to, say, an .mgz file using mri_convert? The error message looks like it can't interpret the file as a NIFTI file (the preceeding float2int message being misleading in this instance, I think).
Nick
On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote:
Hi there,
I am trying to interpolate a volume of tstats to the average surface with mri_vol2surf but I am getting the error below. Does mri_vol2surf take all the inputs that mri_convert takes? Is this a float2int problem mentioned in the bugs section of the --help? If the latter, what argument should I specify with --float2int? Thanks in advance for your time.
Cheers,
-Morgan
mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average --hemi lh --surf inflated --surfreg lh.sphere.reg --out lh.vbm_surf_results.mgh --srcreg reg.dat srcvol = vbm_results_mni305_tl.nii.gz srcreg = reg.dat srcregold = 0 srcwarp unspecified surf = inflated hemi = lh trgsubject = average surfreg = lh.sphere.reg interp = nearest float2int = round INFO: float2int code = 2 niiRead(): error opening file /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz
ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24 _______________________________________________ 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
oops, no image attached!
Morgan Hough wrote:
Hey Doug,
Sorry, what I meant was between the left and right surfaces like in the image that I attached.
Cheers,
-Morgan
Doug Greve wrote:
What do you mean by "between the average surfaces"? Between the white and pial? There are various projection options, eg, you can average between them or take the max. This type of comparison is always a bit ill-posed because the surface in a 3d talairach imbedding space is not that meaningful. You might try mapping your surface-based results into the talairach volume.
doug
Morgan Hough wrote:
Hi Doug,
Multiple versions are always a concern since we have multiple platforms but I have checked them all and I get
$Id: mri_vol2surf.c,v 1.26 2006/02/09 16:31:29 greve Exp $
on all platforms.
I think my problems with the actual output now are due to the problems of trying to project MNI group results onto the average surface - sometimes the results fall between the average surfaces. When viewed in tkmedit you can see why it is not mapping all the MNI group results to the surface. Do you think any projection distance changes would make sense to get a rough approx. of what the t-stats are closest to in this case?
Cheers,
-Morgan
Doug Greve wrote:
Morgan Hough wrote:
Hi Nick,
The file looks fine in mri_info and it is convertible to mgz. If I convert it to Analyze (which I can view using fslview) the mri_vol2surf command works. Happy to send the files along if they would be helpful.
Hmmm, that's strange. It's not a float2int issue. It's having problems opening that file. It is strange because it uses exactly the same code that mri_info and mri_convert use to open it. Is is possible that you have mixed versions? Maybe the vol2surf version you have is older?
I was trying to get a rough approximation of MNI152 space group results projected onto the average surface by registering the volumetric group results with FS's mni305 template and using an identity reg.dat as the srcreg. I have done this but the results look wrong. I have checked the registration of the group results to the mni305 template. Is there anything else I could check? Should I be doing this differently?
That sounds correct. If the reg looks ok, then you can load your t map onto fsaverage in tkmedit along with the surfaces and see whether they intersect your activation.
doug
Cheers,
-Morgan
Nick Schmansky wrote:
Morgan,
I'm not so sure this is a float2int problem (but Doug may be able to answer when he gets back next week). Can you read that .nii.gz file with mri_info? Can you convert it to, say, an .mgz file using mri_convert? The error message looks like it can't interpret the file as a NIFTI file (the preceeding float2int message being misleading in this instance, I think).
Nick
On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote:
> Hi there, > > I am trying to interpolate a volume of tstats to the average > surface with mri_vol2surf but I am getting the error below. Does > mri_vol2surf take all the inputs that mri_convert takes? Is this > a float2int problem mentioned in the bugs section of the --help? > If the latter, what argument should I specify with --float2int? > Thanks in advance for your time. > > Cheers, > > -Morgan > > mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject > average --hemi lh --surf inflated --surfreg lh.sphere.reg --out > lh.vbm_surf_results.mgh --srcreg reg.dat > srcvol = vbm_results_mni305_tl.nii.gz > srcreg = reg.dat > srcregold = 0 > srcwarp unspecified > surf = inflated > hemi = lh > trgsubject = average > surfreg = lh.sphere.reg > interp = nearest > float2int = round > INFO: float2int code = 2 > niiRead(): error opening file > /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz > > ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24 > _______________________________________________ > 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
Trying again.
-M
Doug Greve wrote:
oops, no image attached!
Morgan Hough wrote:
Hey Doug,
Sorry, what I meant was between the left and right surfaces like in the image that I attached.
Cheers,
-Morgan
Doug Greve wrote:
What do you mean by "between the average surfaces"? Between the white and pial? There are various projection options, eg, you can average between them or take the max. This type of comparison is always a bit ill-posed because the surface in a 3d talairach imbedding space is not that meaningful. You might try mapping your surface-based results into the talairach volume.
doug
Morgan Hough wrote:
Hi Doug,
Multiple versions are always a concern since we have multiple platforms but I have checked them all and I get
$Id: mri_vol2surf.c,v 1.26 2006/02/09 16:31:29 greve Exp $
on all platforms.
I think my problems with the actual output now are due to the problems of trying to project MNI group results onto the average surface - sometimes the results fall between the average surfaces. When viewed in tkmedit you can see why it is not mapping all the MNI group results to the surface. Do you think any projection distance changes would make sense to get a rough approx. of what the t-stats are closest to in this case?
Cheers,
-Morgan
Doug Greve wrote:
Morgan Hough wrote:
Hi Nick,
The file looks fine in mri_info and it is convertible to mgz. If I convert it to Analyze (which I can view using fslview) the mri_vol2surf command works. Happy to send the files along if they would be helpful.
Hmmm, that's strange. It's not a float2int issue. It's having problems opening that file. It is strange because it uses exactly the same code that mri_info and mri_convert use to open it. Is is possible that you have mixed versions? Maybe the vol2surf version you have is older?
I was trying to get a rough approximation of MNI152 space group results projected onto the average surface by registering the volumetric group results with FS's mni305 template and using an identity reg.dat as the srcreg. I have done this but the results look wrong. I have checked the registration of the group results to the mni305 template. Is there anything else I could check? Should I be doing this differently?
That sounds correct. If the reg looks ok, then you can load your t map onto fsaverage in tkmedit along with the surfaces and see whether they intersect your activation.
doug
Cheers,
-Morgan
Nick Schmansky wrote:
> Morgan, > > I'm not so sure this is a float2int problem (but Doug may be > able to > answer when he gets back next week). Can you read that .nii.gz > file > with mri_info? Can you convert it to, say, an .mgz file using > mri_convert? The error message looks like it can't interpret > the file > as a NIFTI file (the preceeding float2int message being > misleading in > this instance, I think). > > Nick > > > On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote: > > >> Hi there, >> >> I am trying to interpolate a volume of tstats to the average >> surface with mri_vol2surf but I am getting the error below. >> Does mri_vol2surf take all the inputs that mri_convert takes? >> Is this a float2int problem mentioned in the bugs section of >> the --help? If the latter, what argument should I specify with >> --float2int? Thanks in advance for your time. >> >> Cheers, >> >> -Morgan >> >> mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject >> average --hemi lh --surf inflated --surfreg lh.sphere.reg --out >> lh.vbm_surf_results.mgh --srcreg reg.dat >> srcvol = vbm_results_mni305_tl.nii.gz >> srcreg = reg.dat >> srcregold = 0 >> srcwarp unspecified >> surf = inflated >> hemi = lh >> trgsubject = average >> surfreg = lh.sphere.reg >> interp = nearest >> float2int = round >> INFO: float2int code = 2 >> niiRead(): error opening file >> /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz >> >> ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24 >> _______________________________________________ >> 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
And it does not intersect the other hemi, I assume? I don't think there's really anthing you can do about it.
doug
Morgan Hough wrote:
Trying again.
-M
Doug Greve wrote:
oops, no image attached!
Morgan Hough wrote:
Hey Doug,
Sorry, what I meant was between the left and right surfaces like in the image that I attached.
Cheers,
-Morgan
Doug Greve wrote:
What do you mean by "between the average surfaces"? Between the white and pial? There are various projection options, eg, you can average between them or take the max. This type of comparison is always a bit ill-posed because the surface in a 3d talairach imbedding space is not that meaningful. You might try mapping your surface-based results into the talairach volume.
doug
Morgan Hough wrote:
Hi Doug,
Multiple versions are always a concern since we have multiple platforms but I have checked them all and I get
$Id: mri_vol2surf.c,v 1.26 2006/02/09 16:31:29 greve Exp $
on all platforms.
I think my problems with the actual output now are due to the problems of trying to project MNI group results onto the average surface - sometimes the results fall between the average surfaces. When viewed in tkmedit you can see why it is not mapping all the MNI group results to the surface. Do you think any projection distance changes would make sense to get a rough approx. of what the t-stats are closest to in this case?
Cheers,
-Morgan
Doug Greve wrote:
Morgan Hough wrote:
> Hi Nick, > > The file looks fine in mri_info and it is convertible to mgz. If > I convert it to Analyze (which I can view using fslview) the > mri_vol2surf command works. Happy to send the files along if > they would be helpful.
Hmmm, that's strange. It's not a float2int issue. It's having problems opening that file. It is strange because it uses exactly the same code that mri_info and mri_convert use to open it. Is is possible that you have mixed versions? Maybe the vol2surf version you have is older?
> > I was trying to get a rough approximation of MNI152 space group > results projected onto the average surface by registering the > volumetric group results with FS's mni305 template and using an > identity reg.dat as the srcreg. I have done this but the results > look wrong. I have checked the registration of the group results > to the mni305 template. Is there anything else I could check? > Should I be doing this differently?
That sounds correct. If the reg looks ok, then you can load your t map onto fsaverage in tkmedit along with the surfaces and see whether they intersect your activation.
doug
> > Cheers, > > -Morgan > > Nick Schmansky wrote: > >> Morgan, >> >> I'm not so sure this is a float2int problem (but Doug may be >> able to >> answer when he gets back next week). Can you read that .nii.gz >> file >> with mri_info? Can you convert it to, say, an .mgz file using >> mri_convert? The error message looks like it can't interpret >> the file >> as a NIFTI file (the preceeding float2int message being >> misleading in >> this instance, I think). >> >> Nick >> >> >> On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote: >> >> >>> Hi there, >>> >>> I am trying to interpolate a volume of tstats to the average >>> surface with mri_vol2surf but I am getting the error below. >>> Does mri_vol2surf take all the inputs that mri_convert takes? >>> Is this a float2int problem mentioned in the bugs section of >>> the --help? If the latter, what argument should I specify with >>> --float2int? Thanks in advance for your time. >>> >>> Cheers, >>> >>> -Morgan >>> >>> mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject >>> average --hemi lh --surf inflated --surfreg lh.sphere.reg >>> --out lh.vbm_surf_results.mgh --srcreg reg.dat >>> srcvol = vbm_results_mni305_tl.nii.gz >>> srcreg = reg.dat >>> srcregold = 0 >>> srcwarp unspecified >>> surf = inflated >>> hemi = lh >>> trgsubject = average >>> surfreg = lh.sphere.reg >>> interp = nearest >>> float2int = round >>> INFO: float2int code = 2 >>> niiRead(): error opening file >>> /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz >>> >>> ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24 >>> _______________________________________________ >>> 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 > >
I am no expert, but if I may make a small suggestion based on the image you have provided? I don't know exactly what you're comparing in your VBM, but if indeed there is on average a difference in *shape* of the cortex between the groups you are comparing, then it is not at all surprising that the areas of significant VBM t- statistic are relatively far from the average surface.
If you can interpret the VBM results as saying that one group is more likely to have cortex in the significant area than the other group, then purely for the sake of what you're trying to do here, you might want to generate an average surface from only the group which is *more* likely to have cortex in the area of significance. Then you *would* expect that average surface to overlap the area of significance.
Then you could project the volume t-stat map onto *that* average surface for the purpose of getting as you say "a rough approximation" of the MNI space results projected onto a surface.
Hope this is of some small benefit...
On Jun 1, 2007, at 11:47 AM, Doug Greve wrote:
And it does not intersect the other hemi, I assume? I don't think there's really anthing you can do about it.
doug
-- -dave---------------------------------------------------------------- All I ask is that the kind of unsolvable that it turns out to be has respectable precedents. -Jerry Fodor
freesurfer@nmr.mgh.harvard.edu
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David Perlman -
Doug Greve -
Morgan Hough -
Nick Schmansky