Hi Eugenio,

just to confirm I understand the currently available options. There are two multispectral strategies (MPRAGE + high res 2D T2, or MPRAGE + 3D FLAIR). It would be great to see if the combo option improves things even further for the subfields (MPRAGE + high res 2D T2 + 3D FLAIR). Is that option at all possible with the available FS version or in the works?

Best,

Jorge

On 05/09/2016 16:13, Iglesias, Eugenio wrote:

The same one; just change the input file and the analysis ID

• T2: recon-all -s mySubject -hippocampal-subfields-T1T2

myT2scan.nii.gz T2

• FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2

myFLAIRscan.nii.gz FLAIR

Cheers,

/Eugenio

Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

...

On 5 Sep 2016, at 15:10, Vaz pandolfo, Renata <rvp8@njit.edu mailto:rvp8@njit.edu> wrote:

Dear FS experts, I have a question about the "segmentation with an additional scan - multispectral segmentation" on the hippocampal sf segmentation, FS dev. 6.0. For controls on which I had already run recon-all -all, I added the T2 sequence with the following command: recon-all -s <subject_name> \ -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>

Now, if I want to do the same thing with FLAIR as the additional input, which flag should I use? Thank you, Renata

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If the T2 is already high-res, and having already the T1, I don’t think that the FLAIR would help much. Cheers, /E

Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 5 Sep 2016, at 16:22, Vaz pandolfo, Renata <rvp8@njit.edumailto:rvp8@njit.edu> wrote:

Dear Jorge,

In my case I am using either T1+T2 or T1+FLAIR. I had no intention of using all three at once, but now I am also wondering if this would be an improvement.

Cheers,

Renata

On Mon, Sep 5, 2016 at 4:54 PM, Jovicich, Jorge <jorge.jovicich@unitn.itmailto:jorge.jovicich@unitn.it> wrote:

Hi Eugenio,

just to confirm I understand the currently available options. There are two multispectral strategies (MPRAGE + high res 2D T2, or MPRAGE + 3D FLAIR). It would be great to see if the combo option improves things even further for the subfields (MPRAGE + high res 2D T2 + 3D FLAIR). Is that option at all possible with the available FS version or in the works?

Best,

Jorge

On 05/09/2016 16:13, Iglesias, Eugenio wrote: The same one; just change the input file and the analysis ID

- T2: recon-all -s mySubject -hippocampal-subfields-T1T2 myT2scan.nii.gz T2

- FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2 myFLAIRscan.nii.gz FLAIR

Cheers,

/Eugenio

Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.comhttp://www.jeiglesias.com/ http://cmictig.cs.ucl.ac.uk/

On 5 Sep 2016, at 15:10, Vaz pandolfo, Renata <rvp8@njit.edumailto:rvp8@njit.edu> wrote:

Dear FS experts,

I have a question about the "segmentation with an additional scan - multispectral segmentation" on the hippocampal sf segmentation, FS dev. 6.0.

For controls on which I had already run recon-all -all, I added the T2 sequence with the following command:

recon-all -s <subject_name> \ -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>

Now, if I want to do the same thing with FLAIR as the additional input, which flag should I use?

Thank you,

Renata

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

-- Jorge Jovicich, Ph.D.

MR Lab Head Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy

Telephone: +39-0461-28tel:%2B39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich@unitn.itmailto:jorge.jovicich@unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

Hi,

I have a short question about the additional T2 scan as well.

If I perform the full recon-all; recon-all -s mySubject -i myT1.nii -T2 myT2.nii -T2pial -all -hippocampal-subfields-T1T2 do I still have to precise myT2scan.nii.gz T2 for using the t2 for the hippocampal subfields as well ? or it will automatically take the t2 precised for the t2pial ?

Cheers, Pierre

On Mon, Sep 5, 2016 at 4:13 PM, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:

The same one; just change the input file and the analysis ID

• T2: recon-all -s mySubject -hippocampal-subfields-T1T2

myT2scan.nii.gz T2

• FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2

myFLAIRscan.nii.gz FLAIR

Cheers,

/Eugenio

Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 5 Sep 2016, at 15:10, Vaz pandolfo, Renata rvp8@njit.edu wrote:

Dear FS experts,

I have a question about the "segmentation with an additional scan - multispectral segmentation" on the hippocampal sf segmentation, FS dev. 6.0.

For controls on which I had already run recon-all -all, I added the T2 sequence with the following command:

recon-all -s <subject_name> \ -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>

Now, if I want to do the same thing with FLAIR as the additional input, which flag should I use?

Thank you,

Renata

---

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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.

ok thanks.

Cheers, Pierre

On Mon, Sep 19, 2016 at 3:17 PM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

Yes, you have so specify it separately. Cheers, /Eugenio

Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 19 Sep 2016, at 14:13, pierre deman deman.pierre@gmail.com wrote:

Hi,

I have a short question about the additional T2 scan as well.

If I perform the full recon-all; recon-all -s mySubject -i myT1.nii -T2 myT2.nii -T2pial -all -hippocampal-subfields-T1T2 do I still have to precise myT2scan.nii.gz T2 for using the t2 for the hippocampal subfields as well ? or it will automatically take the t2 precised for the t2pial ?

Cheers, Pierre

On Mon, Sep 5, 2016 at 4:13 PM, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:

...

The same one; just change the input file and the analysis ID

• T2: recon-all -s mySubject -hippocampal-subfields-T1T2

myT2scan.nii.gz T2

• FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2

myFLAIRscan.nii.gz FLAIR

Cheers,

/Eugenio

Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 5 Sep 2016, at 15:10, Vaz pandolfo, Renata rvp8@njit.edu wrote:

Dear FS experts,

I have a question about the "segmentation with an additional scan - multispectral segmentation" on the hippocampal sf segmentation, FS dev. 6.0.

For controls on which I had already run recon-all -all, I added the T2 sequence with the following command:

recon-all -s <subject_name> \ -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>

Now, if I want to do the same thing with FLAIR as the additional input, which flag should I use?

Thank you,

Renata

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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.

-- DEMAN Pierre Mobile : +33 7 82 57 80 94