Dear Freesurfer experts,
We are facing a problem in our study and would need your advice on it. We want to get an accurate measurement for the cortical thickness from our MS patients data. For that we are using 3D T1 and FLAIR (recon-all will be used with the FLAIR option so that we can a more accurate pial surface). However, we were wondering if running recon-all on the raw data would lead to some errors specially because of the juxtacortical lesions or not. Or, is it better to first apply a lesion filling using our lesion mask ? I should specify that we will use the longitudinal pipeline if it is of any use.
Thank you all.
Ismail
PhD candidate Neurocentre Magendie, INSERM Bordeaux, France
I Ismail
yes, if you have juxtacortical lesions you should label them as such in the aseg, then I think it should work
cheers Bruce On Fri, 9 Dec 2016, Ismail Koubiyr wrote:
Dear Freesurfer experts, We are facing a problem in our study and would need your advice on it. We want to get an accurate measurement for the cortical thickness from our MS patients data. For that we are using 3D T1 and FLAIR (recon-all will be used with the FLAIR option so that we can a more accurate pial surface). However, we were wondering if running recon-all on the raw data would lead to some errors specially because of the juxtacortical lesions or not. Or, is it better to first apply a lesion filling using our lesion mask ? I should specify that we will use the longitudinal pipeline if it is of any use.
Thank you all.
Ismail
PhD candidate Neurocentre Magendie, INSERM Bordeaux, France
Hi Bruce,
Thanks for your answer. What do you think would be better, run recon-all on the original data (with lesions) then edit the aseg for the juxtacortical lesions or use a lesion filling on the T1 and then run recon-all on it. Thanks again.
Cheers,
Ismail
PhD candidate Neurocentre Magendie, INSERM Bordeaux, France
2016-12-09 22:58 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
I Ismail
yes, if you have juxtacortical lesions you should label them as such in the aseg, then I think it should work
cheers Bruce On Fri, 9 Dec 2016, Ismail Koubiyr wrote:
Dear Freesurfer experts, We are facing a problem in our study and would need your advice on it. We want to get an accurate measurement for the cortical thickness from
our
MS patients data. For that we are using 3D T1 and FLAIR (recon-all will
be
used with the FLAIR option so that we can a more accurate pial surface). However, we were wondering if running recon-all on the raw data would
lead
to some errors specially because of the juxtacortical lesions or not.
Or, is
it better to first apply a lesion filling using our lesion mask ? I should specify that we will use the longitudinal pipeline if it is of
any
use.
Thank you all.
Ismail
PhD candidate Neurocentre Magendie, INSERM Bordeaux, France
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the former I think, but it's an empirical question Bruce On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
Hi Bruce, Thanks for your answer. What do you think would be better, run recon-all on the original data (with lesions) then edit the aseg for the juxtacortical lesions or use a lesion filling on the T1 and then run recon-all on it. Thanks again.
Cheers,
Ismail
PhD candidate Neurocentre Magendie, INSERM Bordeaux, France
2016-12-09 22:58 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: I Ismail
yes, if you have juxtacortical lesions you should label them as such in the aseg, then I think it should work cheers Bruce On Fri, 9 Dec 2016, Ismail Koubiyr wrote: > Dear Freesurfer experts, > We are facing a problem in our study and would need your advice on it. > We want to get an accurate measurement for the cortical thickness from our > MS patients data. For that we are using 3D T1 and FLAIR (recon-all will be > used with the FLAIR option so that we can a more accurate pial surface). > However, we were wondering if running recon-all on the raw data would lead > to some errors specially because of the juxtacortical lesions or not. Or, is > it better to first apply a lesion filling using our lesion mask ? > I should specify that we will use the longitudinal pipeline if it is of any > use. > > Thank you all. > > Ismail > > PhD candidate > Neurocentre Magendie, INSERM > Bordeaux, France > >
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Would you please give me the reasons why the former would be better ?
Ismail
PhD candidate Neurocentre Magendie, INSERM Bordeaux, France
2016-12-12 15:47 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
the former I think, but it's an empirical question Bruce On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
Hi Bruce, Thanks for your answer. What do you think would be better, run recon-all on the original data
(with
lesions) then edit the aseg for the juxtacortical lesions or use a lesion filling on the T1 and then run recon-all on it. Thanks again.
Cheers,
Ismail
PhD candidate Neurocentre Magendie, INSERM Bordeaux, France
2016-12-09 22:58 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: I Ismail
yes, if you have juxtacortical lesions you should label them as such in the aseg, then I think it should work cheers Bruce On Fri, 9 Dec 2016, Ismail Koubiyr wrote: > Dear Freesurfer experts, > We are facing a problem in our study and would need your advice on it. > We want to get an accurate measurement for the cortical thickness from our > MS patients data. For that we are using 3D T1 and FLAIR (recon-all will be > used with the FLAIR option so that we can a more accurate pial surface). > However, we were wondering if running recon-all on the raw data would lead > to some errors specially because of the juxtacortical lesions or not. Or, is > it better to first apply a lesion filling using our lesion mask ? > I should specify that we will use the longitudinal pipeline if it is of any > use. > > Thank you all. > > Ismail > > PhD candidate > Neurocentre Magendie, INSERM > Bordeaux, France > >
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because filling in the T1 may cause artifacts On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
Would you please give me the reasons why the former would be better ? Ismail
PhD candidate Neurocentre Magendie, INSERM Bordeaux, France
2016-12-12 15:47 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: the former I think, but it's an empirical question Bruce On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
> Hi Bruce, > Thanks for your answer. > What do you think would be better, run recon-all on the original data (with > lesions) then edit the aseg for the juxtacortical lesions or use a lesion > filling on the T1 and then run recon-all on it. > Thanks again. > > Cheers, > > Ismail > > PhD candidate > Neurocentre Magendie, INSERM > Bordeaux, France > > 2016-12-09 22:58 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: > I Ismail > > yes, if you have juxtacortical lesions you should label them as > such in > the aseg, then I think it should work > > cheers > Bruce > On Fri, 9 Dec 2016, Ismail Koubiyr > wrote: > > > Dear Freesurfer experts, > > We are facing a problem in our study and would need your > advice on it. > > We want to get an accurate measurement for the cortical > thickness from our > > MS patients data. For that we are using 3D T1 and FLAIR > (recon-all will be > > used with the FLAIR option so that we can a more accurate pial > surface). > > However, we were wondering if running recon-all on the raw > data would lead > > to some errors specially because of the juxtacortical lesions > or not. Or, is > > it better to first apply a lesion filling using our lesion > mask ? > > I should specify that we will use the longitudinal pipeline if > it is of any > > use. > > > > Thank you all. > > > > Ismail > > > > PhD candidate > > Neurocentre Magendie, INSERM > > Bordeaux, France > > > > > _______________________________________________ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Alright, thanks a lot for your help Bruce.
Best,
Ismail
PhD candidate Neurocentre Magendie, INSERM Bordeaux, France
2016-12-12 17:33 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
because filling in the T1 may cause artifacts
On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
Would you please give me the reasons why the former would be better ?
Ismail
PhD candidate Neurocentre Magendie, INSERM Bordeaux, France
2016-12-12 15:47 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: the former I think, but it's an empirical question Bruce On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
> Hi Bruce, > Thanks for your answer. > What do you think would be better, run recon-all on the originaldata (with > lesions) then edit the aseg for the juxtacortical lesions or use a lesion > filling on the T1 and then run recon-all on it. > Thanks again. > > Cheers, > > Ismail > > PhD candidate > Neurocentre Magendie, INSERM > Bordeaux, France > > 2016-12-09 22:58 GMT+01:00 Bruce Fischl < fischl@nmr.mgh.harvard.edu>: > I Ismail > > yes, if you have juxtacortical lesions you should label them as > such in > the aseg, then I think it should work > > cheers > Bruce > On Fri, 9 Dec 2016, Ismail Koubiyr > wrote: > > > Dear Freesurfer experts, > > We are facing a problem in our study and would need your > advice on it. > > We want to get an accurate measurement for the cortical > thickness from our > > MS patients data. For that we are using 3D T1 and FLAIR > (recon-all will be > > used with the FLAIR option so that we can a more accurate pial > surface). > > However, we were wondering if running recon-all on the raw > data would lead > > to some errors specially because of the juxtacortical lesions > or not. Or, is > > it better to first apply a lesion filling using our lesion > mask ? > > I should specify that we will use the longitudinal pipeline if > it is of any > > use. > > > > Thank you all. > > > > Ismail > > > > PhD candidate > > Neurocentre Magendie, INSERM > > Bordeaux, France > > > > > _______________________________________________ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
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