Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine
Hi Anastasia Thanks a lot for your very nice talk today. I would have another question on top of the one below. I have looked at the formula to calculate the total motion index, and for the third motion parameter (percentage of slice with signal drop-out), all subjects except 2 had a 0 value. So in the formula, I would not be able to calculate the motion factor for this parameter because median, upper and lower quartile are all 0, is that correct (it would make (x-0/0-0))? Thanks for your help Celine
Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine
-- Celine Louapre, MD-PhD, Research Fellow at Massachusetts General Hospital Department of Radiology, MGH
Building 149, Room 2301 13th Street Charlestown, MA 02129 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Celine - You're very welcome!
If this particular motion measure is identical for pretty much all your subjects, there is no point in including it. So you can just use the other 3 motion measures.
a.y
On Wed, 12 Feb 2014, Celine Louapre wrote:
Hi Anastasia Thanks a lot for your very nice talk today. I would have another question on top of the one below. I have looked at the formula to calculate the total motion index, and for the third motion parameter (percentage of slice with signal drop-out), all subjects except 2 had a 0 value. So in the formula, I would not be able to calculate the motion factor for this parameter because median, upper and lower quartile are all 0, is that correct (it would make (x-0/0-0))? Thanks for your help Celine
Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine
-- Celine Louapre, MD-PhD, Research Fellow at Massachusetts General Hospital Department of Radiology, MGH
Building 149, Room 2301 13th Street Charlestown, MA 02129 _______________________________________________ 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 Celine - That's an interesting question. There's nothing implemented in there right now that would allow you to skip part of the tract in the along-the-tract stats. One (not very elegant) way to try to do something like this is:
1. Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume to zero. (You'll want to save the original volume under some other name for backup first.) If you want the same for the diffusivities, repeat for the also for the MD, L1, L2, L3 volumes.
2. Run the dmri_pathstats command line that you'll find in trac-all.log for that subject.
This will regenerate all the pathstats.* files, but now the parts of the tract that go through the lesions will have zero values (or very low, if they're mixed in with some neighboring voxels).
Let us know if this worked! If not I may be able to implement something.
a.y
On Tue, 11 Feb 2014, Celine Louapre wrote:
Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine
Hi Anastasia I have finally managed to coregister and resample all lesion masks on DTI images :-), and as you suggested I set the lesion voxels to 0 in dtifit_FA.nii.gz (as well as L1 L2 L3 and MD volumes)
Then the command I found in the trac-all log was the one below (where TRACT is the full name of the tract and SHORT_TRACT is the short name)
./freesurfer-stable5_3_0-05152013/bin/dmri_pathstats --intrc ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]} --dtbase ${PATH_3T}${SUBJECTS_3T[$subj]}/dmri/dtifit --path ${SHORT_TRACT[$num_tract]} --subj ${SUBJECTS_3T[$subj]} --out ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.overall.txt --outvox ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.byvoxel.txt
However I got this error message and couldn't find in the log file how to set the output type ERROR: fio_pushd: ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr ERROR: fio_pushd: ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr ERROR: must specify at least one type of output
Would you have some idea about that? Thank you very much Celine
Hi Celine - That's an interesting question. There's nothing implemented in there right now that would allow you to skip part of the tract in the along-the-tract stats. One (not very elegant) way to try to do something like this is:
- Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume to zero.
(You'll want to save the original volume under some other name for backup first.) If you want the same for the diffusivities, repeat for the also for the MD, L1, L2, L3 volumes.
- Run the dmri_pathstats command line that you'll find in trac-all.log
for that subject.
This will regenerate all the pathstats.* files, but now the parts of the tract that go through the lesions will have zero values (or very low, if they're mixed in with some neighboring voxels).
Let us know if this worked! If not I may be able to implement something.
a.y
On Tue, 11 Feb 2014, Celine Louapre wrote:
Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine
Hi Celine - This command assumes that --intrc is a tracula output directory, containing all the files that tracula saves in such a directory. What are you trying to get stats from?
a.y
On Mon, 3 Mar 2014, Celine Louapre wrote:
Hi Anastasia I have finally managed to coregister and resample all lesion masks on DTI images :-), and as you suggested I set the lesion voxels to 0 in dtifit_FA.nii.gz (as well as L1 L2 L3 and MD volumes)
Then the command I found in the trac-all log was the one below (where TRACT is the full name of the tract and SHORT_TRACT is the short name)
./freesurfer-stable5_3_0-05152013/bin/dmri_pathstats --intrc ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]} --dtbase ${PATH_3T}${SUBJECTS_3T[$subj]}/dmri/dtifit --path ${SHORT_TRACT[$num_tract]} --subj ${SUBJECTS_3T[$subj]} --out ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.overall.txt --outvox ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.byvoxel.txt
However I got this error message and couldn't find in the log file how to set the output type ERROR: fio_pushd: ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr ERROR: fio_pushd: ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr ERROR: must specify at least one type of output
Would you have some idea about that? Thank you very much Celine
Hi Celine - That's an interesting question. There's nothing implemented in there right now that would allow you to skip part of the tract in the along-the-tract stats. One (not very elegant) way to try to do something like this is:
- Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume to zero.
(You'll want to save the original volume under some other name for backup first.) If you want the same for the diffusivities, repeat for the also for the MD, L1, L2, L3 volumes.
- Run the dmri_pathstats command line that you'll find in trac-all.log
for that subject.
This will regenerate all the pathstats.* files, but now the parts of the tract that go through the lesions will have zero values (or very low, if they're mixed in with some neighboring voxels).
Let us know if this worked! If not I may be able to implement something.
a.y
On Tue, 11 Feb 2014, Celine Louapre wrote:
Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
oh yes I see, I have renamed the dpath/${TRACT[$num_tract]} directories to have a backup, so the name is not correct anymore. Actually I didn't need to do that, I can just set a different name for the outputs pathpathstats.byvoxel.txt and pathstats.overall.txt Thanks Celine
Hi Celine - This command assumes that --intrc is a tracula output directory, containing all the files that tracula saves in such a directory. What are you trying to get stats from?
a.y
On Mon, 3 Mar 2014, Celine Louapre wrote:
Hi Anastasia I have finally managed to coregister and resample all lesion masks on DTI images :-), and as you suggested I set the lesion voxels to 0 in dtifit_FA.nii.gz (as well as L1 L2 L3 and MD volumes)
Then the command I found in the trac-all log was the one below (where TRACT is the full name of the tract and SHORT_TRACT is the short name)
./freesurfer-stable5_3_0-05152013/bin/dmri_pathstats --intrc ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]} --dtbase ${PATH_3T}${SUBJECTS_3T[$subj]}/dmri/dtifit --path ${SHORT_TRACT[$num_tract]} --subj ${SUBJECTS_3T[$subj]} --out ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.overall.txt --outvox ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.byvoxel.txt
However I got this error message and couldn't find in the log file how to set the output type ERROR: fio_pushd: ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr ERROR: fio_pushd: ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr ERROR: must specify at least one type of output
Would you have some idea about that? Thank you very much Celine
Hi Celine - That's an interesting question. There's nothing implemented in there right now that would allow you to skip part of the tract in the along-the-tract stats. One (not very elegant) way to try to do something like this is:
- Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume to zero.
(You'll want to save the original volume under some other name for backup first.) If you want the same for the diffusivities, repeat for the also for the MD, L1, L2, L3 volumes.
- Run the dmri_pathstats command line that you'll find in trac-all.log
for that subject.
This will regenerate all the pathstats.* files, but now the parts of the tract that go through the lesions will have zero values (or very low, if they're mixed in with some neighboring voxels).
Let us know if this worked! If not I may be able to implement something.
a.y
On Tue, 11 Feb 2014, Celine Louapre wrote:
Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine
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freesurfer@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Celine Louapre