Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Dear Doug,
Thank you for your email. Following up on our previous discussions:
1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line "set fsvol = brain mask" (without quotes) at the beginning of the section "#Convert reference to analyze" the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works.
2) when you suggested I run bbregister on the lowb.nii file, was it because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running
3) for the mri_vol2vol step - I had to change targ to fstarg, and I left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv
4) I would like to get the segmentations from aparc+aseg.mgz as the areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats
but then I received this error:
ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256 * * *So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.*
Any ideas on how to proceed?
Thanks,
Sal
On Sat, May 25, 2013 at 11:51 AM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
On 5/25/13 1:39 PM, Salil Soman wrote:
Thank you Doug.
Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following:
*1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.*
bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat
That is right, but add --t2 (since it is t2 weighted).
*2) Use mri_vol2vol and the registration to map the ADC map to the anatomical*
mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg
Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff).
*3) use mri_segstats to extract the values*
*mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats
The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add "--seg-erode 1" to erode the segmentations by a voxel. This helps to prevent partial voluming.
doug
Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table?
I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be?
Best wishes,
Sal
On Sat, May 25, 2013 at 10:06 AM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug
ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks!
On 5/25/13 1:03 PM, Salil Soman wrote:
Dear Dr. Greve,
Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the segmentation from the aseg (or aparc+aseg) file to output a mean ADC value for each anatomic area segmented?
Thank you for your time and consideration.
Best wishes,
Sal
Salil Soman, MD, MS
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.
Hi - I realize that the --inv tag was still in my commands for mr_vol2vol (causing the target and the moving image to be swapped). Removing the --inv tag gave me a new volume normalized to aparc+aseg.nii, and so I was able to then run mri_segstats using the following command:
mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_906_aparc_aseg.stats
Thanks!
-S
On Sun, May 26, 2013 at 11:11 AM, Salil Soman salsoman@stanford.edu wrote:
Dear Doug,
Thank you for your email. Following up on our previous discussions:
- *bbregister fail *- this was happening because of error from
fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line "set fsvol = brain mask" (without quotes) at the beginning of the section "#Convert reference to analyze" the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works.
- when you suggested I run bbregister on the lowb.nii file, was it
because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running
- for the mri_vol2vol step - I had to change targ to fstarg, and I left
out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv
- I would like to get the segmentations from aparc+aseg.mgz as the areas
where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats
but then I received this error:
ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256
*So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.*
Any ideas on how to proceed?
Thanks,
Sal
On Sat, May 25, 2013 at 11:51 AM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
On 5/25/13 1:39 PM, Salil Soman wrote:
Thank you Doug.
Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following:
*1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.*
bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat
That is right, but add --t2 (since it is t2 weighted).
*2) Use mri_vol2vol and the registration to map the ADC map to the anatomical*
mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg
Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff).
*3) use mri_segstats to extract the values*
*mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats
The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add "--seg-erode 1" to erode the segmentations by a voxel. This helps to prevent partial voluming.
doug
Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table?
I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be?
Best wishes,
Sal
On Sat, May 25, 2013 at 10:06 AM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote:
Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug
ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks!
On 5/25/13 1:03 PM, Salil Soman wrote:
Dear Dr. Greve,
Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the segmentation from the aseg (or aparc+aseg) file to output a mean ADC value for each anatomic area segmented?
Thank you for your time and consideration.
Best wishes,
Sal
Salil Soman, MD, MS
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.
As I am working with a 3D volume and not an ADC map, should I still use --seg-erode 1 with mr segstats?
Thank
On Sun, May 26, 2013 at 1:11 PM, Salil Soman salsoman@stanford.edu wrote:
Hi - I realize that the --inv tag was still in my commands for mr_vol2vol (causing the target and the moving image to be swapped). Removing the --inv tag gave me a new volume normalized to aparc+aseg.nii, and so I was able to then run mri_segstats using the following command:
mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_906_aparc_aseg.stats
Thanks!
-S
On Sun, May 26, 2013 at 11:11 AM, Salil Soman salsoman@stanford.eduwrote:
Dear Doug,
Thank you for your email. Following up on our previous discussions:
- *bbregister fail *- this was happening because of error from
fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line "set fsvol = brain mask" (without quotes) at the beginning of the section "#Convert reference to analyze" the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works.
- when you suggested I run bbregister on the lowb.nii file, was it
because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running
- for the mri_vol2vol step - I had to change targ to fstarg, and I left
out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv
- I would like to get the segmentations from aparc+aseg.mgz as the areas
where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats
but then I received this error:
ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256
*So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.*
Any ideas on how to proceed?
Thanks,
Sal
On Sat, May 25, 2013 at 11:51 AM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote:
On 5/25/13 1:39 PM, Salil Soman wrote:
Thank you Doug.
Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following:
*1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.*
bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat
That is right, but add --t2 (since it is t2 weighted).
*2) Use mri_vol2vol and the registration to map the ADC map to the anatomical*
mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg
Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff).
*3) use mri_segstats to extract the values*
*mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats
The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add "--seg-erode 1" to erode the segmentations by a voxel. This helps to prevent partial voluming.
doug
Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table?
I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be?
Best wishes,
Sal
On Sat, May 25, 2013 at 10:06 AM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote:
Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug
ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks!
On 5/25/13 1:03 PM, Salil Soman wrote:
Dear Dr. Greve,
Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the segmentation from the aseg (or aparc+aseg) file to output a mean ADC value for each anatomic area segmented?
Thank you for your time and consideration.
Best wishes,
Sal
Salil Soman, MD, MS
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.
yes On 5/26/13 4:56 PM, Salil Soman wrote:
As I am working with a 3D volume and not an ADC map, should I still use --seg-erode 1 with mr segstats?
Thank
On Sun, May 26, 2013 at 1:11 PM, Salil Soman <salsoman@stanford.edu mailto:salsoman@stanford.edu> wrote:
Hi - I realize that the --inv tag was still in my commands for mr_vol2vol (causing the target and the moving image to be swapped). Removing the --inv tag gave me a new volume normalized to aparc+aseg.nii, and so I was able to then run mri_segstats using the following command: mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_906_aparc_aseg.stats Thanks! -S On Sun, May 26, 2013 at 11:11 AM, Salil Soman <salsoman@stanford.edu <mailto:salsoman@stanford.edu>> wrote: Dear Doug, Thank you for your email. Following up on our previous discussions: 1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line "set fsvol = brain mask" (without quotes) at the beginning of the section "#Convert reference to analyze" the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works. 2) when you suggested I run bbregister on the lowb.nii file, was it because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv 4) I would like to get the segmentations from aparc+aseg.mgz as the areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats but then I received this error: ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256 * * *So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: On 5/25/13 1:39 PM, Salil Soman wrote:Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.datThat is right, but add --t2 (since it is t2 weighted).*2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-regUse the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff).*3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.statsThe input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add "--seg-erode 1" to erode the segmentations by a voxel. This helps to prevent partial voluming. dougWhere lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be? Best wishes, Sal On Sat, May 25, 2013 at 10:06 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: Dear Dr. Greve, Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the segmentation from the aseg (or aparc+aseg) file to output a mean ADC value for each anatomic area segmented? Thank you for your time and consideration. Best wishes, Sal Salil Soman, MD, MS 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 5/26/13 2:11 PM, Salil Soman wrote:
Dear Doug,
Thank you for your email. Following up on our previous discussions:
- *bbregister fail *- this was happening because of error from
fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line "set fsvol = brain mask" (without quotes) at the beginning of the section "#Convert reference to analyze" the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works.
see previous msg.
- when you suggested I run bbregister on the lowb.nii file, was it
because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running
Oh, I did not realize it was a 2D map. Why do you have a 2D map instead of 3D? That might be hard to get registered. You could have used the ADC or FA. In general, you don't want to use the contrast that you will later be testing as it creates a little bit of circularity. It is not much though, and it should be fine.
- for the mri_vol2vol step - I had to change targ to fstarg, and I
left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv
that maps T1 into the bold space. Is that what you want? If you want to map the bold into the anatomical space, then leave off -inv. This will also solve your problem below doug
- I would like to get the segmentations from aparc+aseg.mgz as the
areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats
but then I received this error:
ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256
*So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.*
Any ideas on how to proceed?
Thanks,
Sal
On Sat, May 25, 2013 at 11:51 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 5/25/13 1:39 PM, Salil Soman wrote:Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.datThat is right, but add --t2 (since it is t2 weighted).*2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-regUse the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff).*3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.statsThe input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add "--seg-erode 1" to erode the segmentations by a voxel. This helps to prevent partial voluming. dougWhere lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be? Best wishes, Sal On Sat, May 25, 2013 at 10:06 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: Dear Dr. Greve, Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the segmentation from the aseg (or aparc+aseg) file to output a mean ADC value for each anatomic area segmented? Thank you for your time and consideration. Best wishes, Sal Salil Soman, MD, MS 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.
Thank you Doug,
I think I initially misinderstood a number of things about this process. I have a 3D GRE volume (I guessed its contrast is closest to BOLD, bbregister set to T1 or T2 seemed to work more poorly). It is not a 2D. I would like to transform the 3D GRE volume into freesurfer space, so mri_segstats can use the segmentations from aparc+aseg.mgz to give back mean intensity values for each anatomic area. I could not find a file called lowb.nii, and so was not sure how to proceed.
1) do I need to use the file you mentioned (lowb.nii) - and if so, where would I find the file?
2) so running "mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat" (note inv left off) should map the 3D volume (Vol_906.nii) into the T1 space?
Thank you for all of your help.
Best wishes,
Sal
On Mon, May 27, 2013 at 7:23 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
On 5/26/13 2:11 PM, Salil Soman wrote:
Dear Doug,
Thank you for your email. Following up on our previous discussions:
- *bbregister fail *- this was happening because of error from
fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line "set fsvol = brain mask" (without quotes) at the beginning of the section "#Convert reference to analyze" the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works.
see previous msg.
- when you suggested I run bbregister on the lowb.nii file, was it
because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running
Oh, I did not realize it was a 2D map. Why do you have a 2D map instead of 3D? That might be hard to get registered. You could have used the ADC or FA. In general, you don't want to use the contrast that you will later be testing as it creates a little bit of circularity. It is not much though, and it should be fine.
- for the mri_vol2vol step - I had to change targ to fstarg, and I left
out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv
that maps T1 into the bold space. Is that what you want? If you want to map the bold into the anatomical space, then leave off -inv. This will also solve your problem below doug
- I would like to get the segmentations from aparc+aseg.mgz as the areas
where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats
but then I received this error:
ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256
*So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.*
Any ideas on how to proceed?
Thanks,
Sal
On Sat, May 25, 2013 at 11:51 AM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
On 5/25/13 1:39 PM, Salil Soman wrote:
Thank you Doug.
Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following:
*1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.*
bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat
That is right, but add --t2 (since it is t2 weighted).
*2) Use mri_vol2vol and the registration to map the ADC map to the anatomical*
mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg
Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff).
*3) use mri_segstats to extract the values*
*mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats
The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add "--seg-erode 1" to erode the segmentations by a voxel. This helps to prevent partial voluming.
doug
Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table?
I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be?
Best wishes,
Sal
On Sat, May 25, 2013 at 10:06 AM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote:
Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug
ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks!
On 5/25/13 1:03 PM, Salil Soman wrote:
Dear Dr. Greve,
Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the segmentation from the aseg (or aparc+aseg) file to output a mean ADC value for each anatomic area segmented?
Thank you for your time and consideration.
Best wishes,
Sal
Salil Soman, MD, MS
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 5/27/13 10:42 PM, Salil Soman wrote:
Thank you Doug,
I think I initially misinderstood a number of things about this process. I have a 3D GRE volume (I guessed its contrast is closest to BOLD, bbregister set to T1 or T2 seemed to work more poorly). It is not a 2D. I would like to transform the 3D GRE volume into freesurfer space, so mri_segstats can use the segmentations from aparc+aseg.mgz to give back mean intensity values for each anatomic area. I could not find a file called lowb.nii, and so was not sure how to proceed.
- do I need to use the file you mentioned (lowb.nii) - and if so,
where would I find the file?
You should look at the on-line tutorial for multimodal integration. I thought you were doing DTI and the "lowb" the the acquistion with bvalue=0.
- so running "mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o
Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat" (note inv left off) should map the 3D volume (Vol_906.nii) into the T1 space?
yes
Thank you for all of your help.
Best wishes,
Sal
On Mon, May 27, 2013 at 7:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 5/26/13 2:11 PM, Salil Soman wrote:Dear Doug, Thank you for your email. Following up on our previous discussions: 1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line "set fsvol = brain mask" (without quotes) at the beginning of the section "#Convert reference to analyze" the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works.see previous msg.2) when you suggested I run bbregister on the lowb.nii file, was it because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up runningOh, I did not realize it was a 2D map. Why do you have a 2D map instead of 3D? That might be hard to get registered. You could have used the ADC or FA. In general, you don't want to use the contrast that you will later be testing as it creates a little bit of circularity. It is not much though, and it should be fine.3) for the mri_vol2vol step - I had to change targ to fstarg, and I left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --invthat maps T1 into the bold space. Is that what you want? If you want to map the bold into the anatomical space, then leave off -inv. This will also solve your problem below doug4) I would like to get the segmentations from aparc+aseg.mgz as the areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.statsbut then I received this error: ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256 * * *So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: On 5/25/13 1:39 PM, Salil Soman wrote:Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.datThat is right, but add --t2 (since it is t2 weighted).*2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-regUse the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff).*3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.statsThe input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add "--seg-erode 1" to erode the segmentations by a voxel. This helps to prevent partial voluming. dougWhere lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be? Best wishes, Sal On Sat, May 25, 2013 at 10:06 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: Dear Dr. Greve, Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the segmentation from the aseg (or aparc+aseg) file to output a mean ADC value for each anatomic area segmented? Thank you for your time and consideration. Best wishes, Sal Salil Soman, MD, MS 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
-
Douglas Greve -
Salil Soman