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Thank you for the prompt answer! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298

On Tue, Jul 30, 2019 at 9:18 AM Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

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Dear Daniel,

Such a script doesn’t exist yet (it’s in the to-do list). The reason why it’s not a straightforward extension of segmentHA_T1.sh is that resampling the anisotropic T2s to a common space is not a good idea, given the differences in orientation. There are ways of getting around this problem; I just haven’t found the time to do it, yet…

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Daniel Callow ddcc2442@gmail.com *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, 29 July 2019 at 21:48 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] segmentHA_T2.sh longitudinal version?

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Hello,

I have recently used segmentHA_T1_long.sh and was pleased with the segmentation results. However, I now have a longitudinal data set that has additional T2 high-resolution scans of the hippocampus as well as T1's. I know there is a segmentHA_T2.sh script to incorporate these types of scans. However, there doesn't seem to be a longitudinal version for this. Is this something that is being worked on? Or is there another reason that T2 should not be used with longitudinal analysis?

Thank you for any advice you can provide,

*Daniel Callow*

*PhD Student, Neuroscience and Cognitive Science*

Exercise for Brain Health Lab

University of Maryland, College Park

*ddcc2442@gmail.com ddcc2442@gmail.com*

443-254-6298 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

I would segment the T2s, but using the longitudinally processed T1s/subjects. Unless the T1s are high-res. Then, segment the T1s ;-)

-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Daniel Callow ddcc2442@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 30 July 2019 at 09:36 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] segmentHA_T2.sh longitudinal version?

External Email - Use Caution In that case, would you suggest one to use segmentHA_T1_long.sh instead of segmentHA_T2.sh (cross-sectional) if one has longitudinal data and T2 high-resolution data? Would one be expected to provide superior results?

Best, Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298

On Tue, Jul 30, 2019 at 9:27 AM Daniel Callow <ddcc2442@gmail.commailto:ddcc2442@gmail.com> wrote: Thank you for the prompt answer! Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298

On Tue, Jul 30, 2019 at 9:18 AM Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution Dear Daniel, Such a script doesn’t exist yet (it’s in the to-do list). The reason why it’s not a straightforward extension of segmentHA_T1.sh is that resampling the anisotropic T2s to a common space is not a good idea, given the differences in orientation. There are ways of getting around this problem; I just haven’t found the time to do it, yet… Cheers, /Eugenio

-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daniel Callow <ddcc2442@gmail.commailto:ddcc2442@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, 29 July 2019 at 21:48 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentHA_T2.sh longitudinal version?

External Email - Use Caution Hello,

I have recently used segmentHA_T1_long.sh and was pleased with the segmentation results. However, I now have a longitudinal data set that has additional T2 high-resolution scans of the hippocampus as well as T1's. I know there is a segmentHA_T2.sh script to incorporate these types of scans. However, there doesn't seem to be a longitudinal version for this. Is this something that is being worked on? Or is there another reason that T2 should not be used with longitudinal analysis?

Thank you for any advice you can provide,

Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer