Hi Martin,

I am now trying to run it through the [CROSS] first, to see the effects.
However, since our longitudinal data is already edited (i.e., in the base)
i was interested to see if it was possible to pass the FLAIR in the
longitudinal runs [LONG], which already have implemented the edited [BASE].

Best,
Kasper

2016-05-17 14:59 GMT+02:00 Martin Reuter <mreu...@nmr.mgh.harvard.edu>:

> Hi Kasper,
>
> if I remember correctly, you need to specify it in the cross and the long
> runs (see my email below). Also could be you need the dev version, I have
> never tested it in 5.3.
>
> Best, Martin
>
>
> On 05/17/2016 03:54 AM, Kasper Jessen wrote:
>
> Unfortunately i do not think it works to pass it directly into a
> longitudinal run. I tried the following, which exited with errors:
>
> recon-all -long d256a d256_base -FLAIR path/flair.nii.gz -autorecon3
> -FLAIRpial
>
> Any suggestions?
>
> Best,
>
> Kasper
>
> 2016-05-13 20:01 GMT+02:00 Martin Reuter <mreu...@nmr.mgh.harvard.edu>:
>
>> Hi Kasper,
>> It should work (I tried it a while ago with the dev version and it did
>> not crash :-). Could not really tell if it helped much either.
>> I don't remember if functionality is available in FS5.3 to include that
>> in a long run. In dev, you would include the T2 for both the cross and long
>> run. The long run then takes the T2 from the cross. Not sure if it works
>> passing it directly into a longitudinal run.
>>
>> Best, Martin
>>
>>
>> On 05/13/2016 08:43 AM, Bruce Fischl wrote:
>>
>> Hi Kasper,
>>
>> I don't see why not, but we haven't done this yet I don't think, so there
>> may be undiscovered bugs.
>> Bruce
>> On Fri, 13 May 2016, Kasper Jessen wrote:
>>
>> Dear FreeSurfer,
>> Currently, we have only manual edited the BASE (the CROSS was left
>> unedited)
>> in an longitudinal data. However, some cortical areas (f.eks. such as the
>> inferior temporal area) are difficult to edit accurately due to image
>> quality. I then read through the release notes (stable v5.2.0) and found
>> that a T2/FLAIR can be used to improve the pial surface.
>>
>> Question: Is it possible to use a T2 and run either -autorecon3 and
>> -T2pial
>> on the [LONG] runs to get extra improvement of the final pial surfaces?
>>
>> Best regards,
>> Kasper Jessen
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>> Martin Reuter, PhD
>> Assistant Professor of Radiology, Harvard Medical School
>> Assistant Professor of Neurology, Harvard Medical School
>> A.A.Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> Research Affiliate, CSAIL, MIT
>> Phone: +1-617-724-5652
>> Web  : http://reuter.mit.edu
>>
>>
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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
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>> but does not contain patient information, please contact the sender and
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>> dispose of the e-mail.
>>
>>
>
>
> --
> Kasper Jessen,
> MD, PhD student
> Center for neuropsychiatric Schizophrenia Research (CNSR)
> Mental Health Centre Glostrup
> Nordre Ringvej 29-67
> 2600 Glostrup
> Tlf.: 24430136
> E-mail: kaspe...@cnsr.dk eller kasper.jes...@regionh.dk
>
>
> _______________________________________________
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  : http://reuter.mit.edu
>
>
> _______________________________________________
> 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.
>
>


-- 
Kasper Jessen,
MD, PhD student
Center for neuropsychiatric Schizophrenia Research (CNSR)
Mental Health Centre Glostrup
Nordre Ringvej 29-67
2600 Glostrup
Tlf.: 24430136
E-mail: kaspe...@cnsr.dk eller kasper.jes...@regionh.dk
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