Hi Lilla,
Many thanks again for your help. In the mean time I checked with echo $FREESURFER_HOME and as I knew my $FREESURFER_HOME is /usr/local/freesurfer Under this directory I have the subjects directory but here unfortunately I am having the cvs_avg35/mri/norm.mgz.
1) Can you please help me find or get the the cvs_avg35/mri/norm.mgz? I saw online the same question was posted on June 2011 but there is no answer for the question online: http://www.opensubscriber.com/message/freesurfer@nmr.mgh.harvard.edu/1550660...
2) Since for my TBSS TBSS study was used by the TBSS the nonlinear registration FNIRT (is about 15 times faster than IRTK on FA data and possibly a little more 'accurate') I would like to use for a Tal space a non-linear talairach registration. Can you please give me some directions on how I can do this? What is the default Tal registration (linear or non-linear) for dt_recon?
3) When dt_recon is aligning the diffusion data in the Tal space is in fact aligning the register.dat data (difussion data already aligned to the structural data) and the output is the fa-tal.nii.gz? If not why I need the register.dat file?
4) So by my understanding each subject will have a file called fa-tal.nii which in fact represents the subject's registration on the Tal-space? How about the mean diffusivity? I don't have only one file for this adc.nii. What if I want to do a non_FA values study on the tal space?
5) I understood that the 'registration.dat' file describes a rigid-body transformation from the diffusion to the structural space and in order to resample the structural volume in the diffusion space, I will need to apply the inverse of this transformation to my input volumes and to use for this the 'mri_vol2vol':
mri_vol2vol --mov $TUTORIAL_DIR/$subj/dtrecon/lowb.nii \ --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \ --inv --interp nearest --o $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat --no-save-reg
Is the register.dat file created by this function mri_vol2vol? I believe the registration between the diffusion and structural space (so the register.dat file) has already been computed as part of the previous pre-processing step so while using the mri_vol2vol as above do I need to use the '--no-save-reg' flag as in the above example or the '--save-reg' flag?
6) To resample the diffusion data of one subject in the CVS space do I need to run after dt_recon the mri_vol2vol as below?
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
Do I need to run the mri_cvs_registration on the structural data in order to get the above .m3z file 'combined_tocvs_avg35_elreg_afteraseg-norm.m3z' before I run the mri_vol2vol?
If I want to have my second registration step done in the Tal space not CVS space since after running dt_recon I am getting the fa-tal.nii.gz and the fa-masked.mgz is this the equivalent file to fa-masked.ANAT+CVS-to-avg35.mgz (if I use the CVS space)? In this case I don't need to run the last mri_vol2vol command?
Sorry for asking so many questions but it is very confusing the online material.
Many thanks! Antonella
From: Lilla Zollei lzollei@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, November 15, 2011 5:11 PM Subject: RE:[Freesurfer] dt_recon registration
Hi Antonella,
- Why I don't have in my $FREESURFER_HOME/subjects the cvs_avg35/mri/norm.mgz? In my subjects directory I only have my subjects and nothing else. How can I get the cvs_avg35/mri/norm.mgz?
$FREESURFER_HOME is different from your $SUBJECTS_DIR. Could you double check?
- Do you believe that for my subjects-all children ages 6-13 the results are gone be OK if I use the talairach registration and re-sampling? As I mentioned in my previous email I would like to do
a two-group study similar with TBSS so to do a statistical analysis on the FA and non_FA data such as mean diffusivity, to see if there are any clusters that may survive by multiple comparisons without any covariant.
Are you referring to a linear or a non-linear talairach registration? It will be you who needs to decide which space to use for analysis. You would want all your data to be well aligned in that space in order to achieve a meaningful group comparison. The decision might also depend on in which space you want to report your final results in.
- Do you have any suggestion regarding which registration is better to be used for this study?
I am not familiar with your study, so it would be hard to say.
- How I can check for each individual subject if the registration worked out well if for example I choose the talairach space?
Do I run:
tkregister2 --mov lowb.nii --reg register.dat --surf or which file is in fact the registered data file? Is the fa-tal.nii.gz or the lowb.nii.gz? You mentioned that the default registration is on talairch space and the I see on dt_recon tutorial that is also doing a registration of lowb to same-subject anatomical so I have two registration done when I run the dt_recon?
dt_recon has two registration steps. One aligns the diffusion data (lowb) to the structural (registration.dat is the default name of the registration file) and the other aligns the diffusion data in the Tal space (the resampled fa file in that space is fa-tal). You can use both freeview and thregister to check the alignment of your volumes.
Lilla
From: Lilla Zollei lzollei@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 14, 2011 4:13 PM Subject: Re: [Freesurfer] dt_recon registration
Hi Antonella,
- I will be very grateful if you can confirm if my coding is write. First can you please let me know if by default dt_recon is re-sample FA to talairch space? In this case because I want to register on CVS should I add the --no-tal flag? I am asking this
question
because after I ran the following command I see in my output directory called P07_dti a file called fa_tal.nii as well as fa_tal.nii.reg.
The talairach registration and re-sampling does take place by default, but that should not affect your further
processing as the fa.nii file (in the native space) is not deleted from the directory. So you can either leave the default settings or you can also use
--no-tal.
- Do I need this files if I want to do a group study for my FA and mean diffusivity, similar to TBSS in FSL?
Are you referring to the tal registration files? If you want to do the group study in the CVS spacem then you will not need the tal registration files.
- Can I use the talairch registration or should I use the CVS?
Depends on where you want to do your analysis.
- Should I add the flag --no-tal?
You can. If you don't you just end up with two additional files.
This is what I was running:
setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR
$FREESURFER_HOME/subjects/DTI_FS/dtrecon
dt_recon --i P07_dti.nii.gz -- b P07.bvals P07.bvects --s P07 --o P07_dti where
P07_dti.nii.gz is my DTI volume P07.bvals P07.bvects are the bvals and bvects for my subject P07 is my structural recons data for my P07 subject
- From the dt_recon --help I understand that dt_recon is doing the registration of lowb to same-subject anatomical using
FSLs flirt (creates mask.nii and register.dat).
mri_vol2vol --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/lowb.nii \ --targ $SUBJECTS_DIR/P07/mri/wmparc.mgz \ --inv --interp nearest --o
$SUBJECTS_DIR/P07/mri/wmparc2diff.mgz \
--reg /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/register.dat --no-save-reg
Actually dt-recon now uses bbregister, but the output of this step is still register.dat. With the above you move the wmparc into the diffusion space.
- Should I run mri_vol2vol to re-sample the structural volume in the diffusion space and register in the CVS space:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \
--mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.mgz \
--o /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
With the above you are going to move your diffusion file (fa) into the CVS space (by implicitely combining a moprh moving the diffusion file to the structural space and then to the CVS space) and not resampling the structural volume in the diffusion space.
- I found online that the default CVS template is cvs_avg35 which is supplied with my FreeSurfer distribution. Can you please tell me in which directory is located or how I can obtain
the cvs_avg35?
It should be
in $FREESURFER_HOME/subjects (as indicated above in your command --targ).
--Lilla _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the
e-mail.
Hi Antonella,
- Can you please help me find or get the the cvs_avg35/mri/norm.mgz? I saw online the same question was posted on June 2011 but there is no answer for the question online:
http://www.opensubscriber.com/message/freesurfer@nmr.mgh.harvard.edu/1550660...
Have you run the cvs_registration code? If you have, then you have to have the template. If you have not, I can make the template subject available for you for download.
- Since for my TBSS TBSS study was used by the TBSS the nonlinear registration FNIRT (is about 15 times faster than IRTK on FA data and possibly a little more 'accurate') I would like to use for a Tal space a non-linear talairach registration. Can you please give
me some directions on how I can do this? What is the default Tal registration (linear or non-linear) for dt_recon?
dt_recon produces a linear registration to the Tal space. If you have ran recon-all on your structural data you should also have access to talairach.m3z that aligns your subject in the fsaverage space.
- When dt_recon is aligning the diffusion data in the Tal space is in fact aligning the register.dat data (difussion data already aligned to the structural data) and the output is the fa-tal.nii.gz? If not why I need the register.dat file?
I don't understand your question, but * register.dat is the registrationfile that encodes the transform going from the diffusion to the structural space. If you want to resample any of your diffusion related files in the structural space you will need to use mri_vol2vol and that file to do so. * fa-tal.nii.gz is a completely different file. It is the fa volume that got resampled in the Tal space using a linear transformation (talairach.xfm via the structural data).
- So by my understanding each subject will have a file called fa-tal.nii which in fact represents the subject's registration on the Tal-space? How about the mean diffusivity? I don't have only one file for this adc.nii. What if I want to do a non_FA values study on
the tal space?
You need to run the follwoing command, replacing fa with the scalar volume of your interest.
set reg = register.dat set fa = fa.nii set fatal = fa-tal.nii.gz set cmd = (mri_vol2vol --reg $reg --tal --mov $fa --o $fatal)
- I understood that the 'registration.dat' file describes a rigid-body transformation from the diffusion to the structural space and in order to resample the structural volume in the diffusion space, I will need to apply the inverse of this transformation to my
input volumes and to use for this the 'mri_vol2vol':
mri_vol2vol --mov $TUTORIAL_DIR/$subj/dtrecon/lowb.nii \ --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \ --inv --interp nearest --o $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat --no-save-reg Is the register.dat file created by this function mri_vol2vol? I believe the registration between the diffusion and structural space (so the register.dat file) has already been computed as part of the previous pre-processing step so while using the mri_vol2vol as above do I need to use the '--no-save-reg' flag as in the above example or the '--save-reg' flag?
register.dat gets created using dt_recon and mri_vol2vol just applies that transform. --no-save-reg just tells the command not to save a copy of the inverse transform that gets applied.
- To resample the diffusion data of one subject in the CVS space do I need to run after dt_recon the mri_vol2vol as below?
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg Do I need to run the mri_cvs_registration on the structural data in order to get the above .m3z file 'combined_tocvs_avg35_elreg_afteraseg-norm.m3z' before I run the mri_vol2vol? If I want to have my second registration step done in the Tal space not CVS space since after running dt_recon I am getting the fa-tal.nii.gz and the fa-masked.mgz is this the equivalent file to fa-masked.ANAT+CVS-to-avg35.mgz (if I use the CVS space)? In this case I don't need to run the last mri_vol2vol command? Sorry for asking so many questions but it is very confusing the online material.
Yes, you will run mri_cvs_register on the structural data and that will compute your m3z file.
fa-masked is in the native diffusion space and fa-tal is in the Talairach space so they are not equivalent with each other, they don't live in the same space.
--Lilla
From: Lilla Zollei lzollei@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, November 15, 2011 5:11 PM Subject: RE:[Freesurfer] dt_recon registration
Hi Antonella,
- Why I don't have in my $FREESURFER_HOME/subjects the cvs_avg35/mri/norm.mgz? In my subjects directory I only have my subjects and nothing else. How can I get the cvs_avg35/mri/norm.mgz?
$FREESURFER_HOME is different from your $SUBJECTS_DIR. Could you double check?
- Do you believe that for my subjects-all children ages 6-13 the results are gone be OK if I use the talairach registration and re-sampling? As I mentioned in my previous email I would like to do
a two-group study similar with TBSS so to do a statistical analysis on the FA and non_FA data such as mean diffusivity, to see if there are any clusters that may survive by multiple comparisons without any covariant.
Are you referring to a linear or a non-linear talairach registration? It will be you who needs to decide which space to use for analysis. You would want all your data to be well aligned in that space in order to achieve a meaningful group comparison. The decision might also depend on in which space you want to report your final results in.
- Do you have any suggestion regarding which registration is better to be used for this study?
I am not familiar with your study, so it would be hard to say.
- How I can check for each individual subject if the registration worked out well if for example I choose the talairach space?
Do I run:
tkregister2 --mov lowb.nii --reg register.dat --surf or which file is in fact the registered data file? Is the fa-tal.nii.gz or the lowb.nii.gz? You mentioned that the default registration is on talairch space and the I see on dt_recon tutorial that is also doing a registration of lowb to same-subject anatomical so I have two registration done when I run the dt_recon?
dt_recon has two registration steps. One aligns the diffusion data (lowb) to the structural (registration.dat is the default name of the registration file) and the other aligns the diffusion data in the Tal space (the resampled fa file in that space is fa-tal). You can use both freeview and thregister to check the alignment of your volumes.
Lilla
_
From: Lilla Zollei lzollei@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 14, 2011 4:13 PM Subject: Re: [Freesurfer] dt_recon registration
Hi Antonella,
- I will be very grateful if you can confirm if my coding is write. First can you please let me know if by default dt_recon is re-sample FA to talairch space? In this case because I want to register on CVS should I add the --no-tal flag? I am asking this
question
because after I ran the following command I see in my output directory called P07_dti a file called fa_tal.nii as well as fa_tal.nii.reg.
The talairach registration and re-sampling does take place by default, but that should not affect your further processing as the fa.nii file (in the native space) is not deleted from the directory. So you can either leave the default settings or you can also use --no-tal.
- Do I need this files if I want to do a group study for my FA and mean diffusivity, similar to TBSS in FSL?
Are you referring to the tal registration files? If you want to do the group study in the CVS spacem then you will not need the tal registration files.
- Can I use the talairch registration or should I use the CVS?
Depends on where you want to do your analysis.
- Should I add the flag --no-tal?
You can. If you don't you just end up with two additional files.
This is what I was running:
setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/DTI_FS/dtrecon
dt_recon --i P07_dti.nii.gz -- b P07.bvals P07.bvects --s P07 --o P07_dti where
P07_dti.nii.gz is my DTI volume P07.bvals P07.bvects are the bvals and bvects for my subject P07 is my structural recons data for my P07 subject
- From the dt_recon --help I understand that dt_recon is doing the registration of lowb to same-subject anatomical using
FSLs flirt (creates mask.nii and register.dat).
mri_vol2vol --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/lowb.nii \ --targ $SUBJECTS_DIR/P07/mri/wmparc.mgz \ --inv --interp nearest --o $SUBJECTS_DIR/P07/mri/wmparc2diff.mgz \ --reg /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/register.dat --no-save-reg
Actually dt-recon now uses bbregister, but the output of this step is still register.dat. With the above you move the wmparc into the diffusion space.
- Should I run mri_vol2vol to re-sample the structural volume in the diffusion space and register in the CVS space:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.mgz \ --o /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
With the above you are going to move your diffusion file (fa) into the CVS space (by implicitely combining a moprh moving the diffusion file to the structural space and then to the CVS space) and not resampling the structural volume in the diffusion space.
- I found online that the default CVS template is cvs_avg35 which is supplied with my FreeSurfer distribution. Can you please tell me in which directory is located or how I can obtain
the cvs_avg35?
It should be in $FREESURFER_HOME/subjects (as indicated above in your command --targ).
--Lilla _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Antonella Kis -
Lilla Zollei