Re: [Freesurfer] Data on the Freesurfer surface
inal functional space. > > > > > > Best wishes, > > > Mason > > > > > > Mason T Wells, MSc > > > PhD student > > > School of Optometry and Vision Sciences > > > & Cardiff University Brain Research > > > Imaging Centre (CUBRIC), School of Psychology > > > Cardiff University > > > Cardiff > > > CF24 4HQ > > > UK > > > > > > Email: wells...@cardiff.ac.uk > > > Tel: 02920 879628 > > > Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> > > > Mason T Wells, MSc > > > Myfyriwr PhD > > > Yr Ysgol Optometreg a Gwyddorau’r Golwg > > > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg > > > Prifysgol Caerdydd > > > Heol Maindy > > > Caerdydd > > > CF24 4HQ > > > DU > > > > > > E-bost: wells...@caerdydd.ac.uk > > > Ffôn: 02920 879628 > > > > > > > > > On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: > > > > > >Hi Mason > > > > > >is your filtered_func file already sampled onto the surface or is it a > > >volume? > > > > > >cheers > > >Bruce > > >On Fri, 17 Apr 2020, Mason Wells wrote: > > > > > >> > > >> External Email - Use Caution > > >> > > >> Hi all, > > >> > > >> > > >> > > >> I am trying to use an analysis package that works on surface based data > > >> (SamSrf). I have ran Feat and have a filtered_func file which is of course > > >> the motion corrected/unwarped version of my EPI. However, I need some advice > > >> on how to get these data onto the Freesurfer surface. I have found this > > >> page, but I wanted to double check this is the most up-to-date pipeline. On > > >> the page it suggests using the same DOF as used in Feat, I use BBR so this > > >> seems a little redundant. Has anyone on these lists got any experience of > > >> getting filtered_func onto the Freesurfer surface? > > >> > > >> > > >> > > >> Thanks in advance, > > >> > > >> Mason > > >> > > >> > > >> > > >> > > >> > > >> Mason T Wells, MSc > > >> > > >> PhD student > > >> > > >> School of Optometry and Vision Sciences > > >> > > >> & Cardiff University Brain Research > > >> > > >> Imaging Centre (CUBRIC), School of Psychology > > >> >
Re: [Freesurfer] Data on the Freesurfer surface
er-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: > > > > > >Hi Mason > > > > > >is your filtered_func file already sampled onto the surface or is it a > > >volume? > > > > > >cheers > > >Bruce > > >On Fri, 17 Apr 2020, Mason Wells wrote: > > > > > >> > > >> External Email - Use Caution > > >> > > >> Hi all, > > >> > > >> > > >> > > >> I am trying to use an analysis package that works on surface based data > > >> (SamSrf). I have ran Feat and have a filtered_func file which is of course > > >> the motion corrected/unwarped version of my EPI. However, I need some advice > > >> on how to get these data onto the Freesurfer surface. I have found this > > >> page, but I wanted to double check this is the most up-to-date pipeline. On > > >> the page it suggests using the same DOF as used in Feat, I use BBR so this > > >> seems a little redundant. Has anyone on these lists got any experience of > > >> getting filtered_func onto the Freesurfer surface? > > >> > > >> > > >> > > >> Thanks in advance, > > >> > > >> Mason > > >> > > >> > > >> > > >> > > >> > > >> Mason T Wells, MSc > > >> > > >> PhD student > > >> > > >> School of Optometry and Vision Sciences > > >> > > >> & Cardiff University Brain Research > > >> > > >> Imaging Centre (CUBRIC), School of Psychology > > >> > > >> Cardiff University > > >> > > >> Cardiff > > >> > > >> CF24 4HQ > > >> > > >> UK > > >> > > >> > > >> > > >> Email: wells...@cardiff.ac.uk > > >> > > >> Tel: 02920 879628 > > >> > > >> Web: Cardiff University webpage > > >> > > >> Mason T Wells, MSc > > >> > > >> Myfyriwr PhD > > >> > > >> Yr Ysgol Optometreg a Gwyddorau’r Golwg > > >> > > >> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol > > >> Seicoleg > > >> > > >> Prifysgol Caerdydd > > >> > > >> Heol Maindy > > >> > > >> Caerdydd > > >> > > >> CF24 4HQ > > >> > > >> DU > > >> > > >> > > >> > > >> E-bost: wells...@caerdydd.ac.uk > > >> > > >> Ffôn: 02920 879628 > > >> > > >> > > >> >
Re: [Freesurfer] Data on the Freesurfer surface
ty > > Cardiff > > CF24 4HQ > > UK > > > > Email: wells...@cardiff.ac.uk > > Tel: 02920 879628 > > Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> > > Mason T Wells, MSc > > Myfyriwr PhD > > Yr Ysgol Optometreg a Gwyddorau’r Golwg > > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg > > Prifysgol Caerdydd > > Heol Maindy > > Caerdydd > > CF24 4HQ > > DU > > > > E-bost: wells...@caerdydd.ac.uk > > Ffôn: 02920 879628 > > > > > > On 17/04/2020, 15:32, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: > > > > oh, then you probably want to use bbreg to register it and mri_vol2surf > > to sample it onto the surface. Doug is the expert on this and can > > add/correct if this is not the whole story :) > > > > cheers > > Bruce > > On Fri, 17 Apr 2020, Mason > > Wells wrote: > > > > >External Email - Use Caution > > > > > > Hi Bruce, > > > > > > The only pre-processing I have done is the motion correction, high pass filtering and distortion correction. So, as far as I know it is still in the volume and in the original functional space. > > > > > > Best wishes, > > > Mason > > > > > > Mason T Wells, MSc > > > PhD student > > > School of Optometry and Vision Sciences > > > & Cardiff University Brain Research > > > Imaging Centre (CUBRIC), School of Psychology > > > Cardiff University > > > Cardiff > > > CF24 4HQ > > > UK > > > > > > Email: wells...@cardiff.ac.uk > > > Tel: 02920 879628 > > > Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> > > > Mason T Wells, MSc > > > Myfyriwr PhD > > > Yr Ysgol Optometreg a Gwyddorau’r Golwg > > > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg > > > Prifysgol Caerdydd > > > Heol Maindy > > > Caerdydd > > > CF24 4HQ > > > DU > > > > > > E-bost: wells...@caerdydd.ac.uk > > > Ffôn: 02920 879628 > > > > > > > > > On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: > > > > > >Hi Mason > > > > > >is your filtered_func file already sampled onto the surface or is it a > > >volume? > > > > > >cheers > > >Bruce > > >On Fri, 17 Apr 2020, Mason Wells wrote: > > > > > >> > > >> External Email - Use Caution > > >> > > >> Hi all, > > >> > > >> > > >> > > >> I am trying to use an analysis package that works on surface based data > > >> (SamSrf). I have ran Feat and have a filtered_func file which is of course > > >> the motion corrected/unwarped version of my EPI. However, I need some advice > > >> on how to get these data onto the Freesurfer surface. I have found this > > >> page, but I wanted to double check this is the most up-to-date pipeline. On > > >> the page it suggests using the same DOF as used in Feat, I u
Re: [Freesurfer] Data on the Freesurfer surface
t; >External Email - Use Caution > > > > > > Hi Bruce, > > > > > > The only pre-processing I have done is the motion correction, > high pass filtering and distortion correction. So, as far as I know it is > still in the volume and in the original functional space. > > > > > > Best wishes, > > > Mason > > > > > > Mason T Wells, MSc > > > PhD student > > > School of Optometry and Vision Sciences > > > & Cardiff University Brain Research > > > Imaging Centre (CUBRIC), School of Psychology > > > Cardiff University > > > Cardiff > > > CF24 4HQ > > > UK > > > > > > Email: wells...@cardiff.ac.uk > > > Tel: 02920 879628 > > > Web: Cardiff University webpage > <https://www.cardiff.ac.uk/people/research-students/view/974214-> > > > Mason T Wells, MSc > > > Myfyriwr PhD > > > Yr Ysgol Optometreg a Gwyddorau’r Golwg > > > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd > (CUBRIC), Yr Ysgol Seicoleg > > > Prifysgol Caerdydd > > > Heol Maindy > > > Caerdydd > > > CF24 4HQ > > > DU > > > > > > E-bost: wells...@caerdydd.ac.uk > > > Ffôn: 02920 879628 > > > > > > > > > On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl" of fis...@nmr.mgh.harvard.edu> wrote: > > > > > >Hi Mason > > > > > >is your filtered_func file already sampled onto the surface > or is it a > > >volume? > > > > > >cheers > > >Bruce > > >On Fri, 17 Apr 2020, Mason Wells wrote: > > > > > >> > > >> External Email - Use Caution > > >> > > >> Hi all, > > >> > > >> > > >> > > >> I am trying to use an analysis package that works on > surface based data > > >> (SamSrf). I have ran Feat and have a filtered_func file > which is of course > > >> the motion corrected/unwarped version of my EPI. However, > I need some advice > > >> on how to get these data onto the Freesurfer surface. I > have found this > > >> page, but I wanted to double check this is the most > up-to-date pipeline. On > > >> the page it suggests using the same DOF as used in Feat, I > use BBR so this > > >> seems a little redundant. Has anyone on these lists got > any experience of > > >> getting filtered_func onto the Freesurfer surface? > > >> > > >> > > >> > > >> Thanks in advance, > > >> > > >> Mason > > >> > > >> > > >> > > >> > > >> > > >> Mason T Wells, MSc > > >> > > >> PhD student > > >> > > >> School of Optometry and Vision Sciences > > >> > > >> & Cardiff University Brain Research > > >> > > >> Imaging Centre (CUBRIC), School of Psychology > > >> > > >> Cardiff University > > >> > > >> Cardiff > > >> > > >> CF24 4HQ > > >> > > >> UK > > >> > > >> > > >> > > >> Email: wells...@cardiff.ac.uk > > >> > > >> Tel: 02920 879628 > > >> > > >> Web: Cardiff Un
Re: [Freesurfer] Data on the Freesurfer surface
gt; Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> > > Mason T Wells, MSc > > Myfyriwr PhD > > Yr Ysgol Optometreg a Gwyddorau’r Golwg > > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg > > Prifysgol Caerdydd > > Heol Maindy > > Caerdydd > > CF24 4HQ > > DU > > > > E-bost: wells...@caerdydd.ac.uk > > Ffôn: 02920 879628 > > > > > > On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: > > > >Hi Mason > > > >is your filtered_func file already sampled onto the surface or is it a > >volume? > > > >cheers > >Bruce > >On Fri, 17 Apr 2020, Mason Wells wrote: > > > > > > >> External Email - Use Caution > >> > >> Hi all, > >> > >> > >> > >> I am trying to use an analysis package that works on surface based data > >> (SamSrf). I have ran Feat and have a filtered_func file which is of course > >> the motion corrected/unwarped version of my EPI. However, I need some advice > >> on how to get these data onto the Freesurfer surface. I have found this > >> page, but I wanted to double check this is the most up-to-date pipeline. On > >> the page it suggests using the same DOF as used in Feat, I use BBR so this > >> seems a little redundant. Has anyone on these lists got any experience of > >> getting filtered_func onto the Freesurfer surface? > >> > >> > >> > >> Thanks in advance, > >> > >> Mason > >> > >> > >> > >> > >> > >> Mason T Wells, MSc > >> > >> PhD student > >> > >> School of Optometry and Vision Sciences > >> > >> & Cardiff University Brain Research > >> > >> Imaging Centre (CUBRIC), School of Psychology > >> > >> Cardiff University > >> > >> Cardiff > >> > >> CF24 4HQ > >> > >> UK > >> > >> > >> > >> Email: wells...@cardiff.ac.uk > >> > >> Tel: 02920 879628 > >> > >> Web: Cardiff University webpage > >> > >> Mason T Wells, MSc > >> > >> Myfyriwr PhD > >> > >> Yr Ysgol Optometreg a Gwyddorau’r Golwg > >> > >> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol > >> Seicoleg > >> > >> Prifysgol Caerdydd > >> > >> Heol Maindy > >> > >> Caerdydd > >> > >> CF24 4HQ > >> > >> DU > >> > >> > >> > >> E-bost: wells...@caerdydd.ac.uk > >> > >> Ffôn: 02920 879628 > >> > >> > >> > >> > >> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurferdata=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Caac15b24194e4daf083208d7e2ee1141%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227384425792122sdata=vxb0%2B702WAjNNOm%2BiL6RswrLb1IgoZg1itj15%2F15pZ4%3Dreserved=0 > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurferdata=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Caac15b24194e4daf083208d7e2ee1141%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227384425792122sdata=vxb0%2B702WAjNNOm%2BiL6RswrLb1IgoZg1itj15%2F15pZ4%3Dreserved=0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurferdata=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Caac15b24194e4daf083208d7e2ee1141%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227384425792122sdata=vxb0%2B702WAjNNOm%2BiL6RswrLb1IgoZg1itj15%2F15pZ4%3Dreserved=0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Data on the Freesurfer surface
Yes, use the template.nii.gz as the registration target. A long time ago we used to have some wrappers that would operate directly on feat folders. Not sure if they still work but, check out https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer On 4/17/2020 10:43 AM, Mason Wells wrote: > External Email - Use Caution > > Great, thanks again Bruce. > Doug, can you confirm this is the process for taking a filtered_func file and > getting it onto the freesurfer surface ready for analysis? > > Mason T Wells, MSc > PhD student > School of Optometry and Vision Sciences > & Cardiff University Brain Research > Imaging Centre (CUBRIC), School of Psychology > Cardiff University > Cardiff > CF24 4HQ > UK > > Email: wells...@cardiff.ac.uk > Tel: 02920 879628 > Web: Cardiff University webpage > <https://www.cardiff.ac.uk/people/research-students/view/974214-> > Mason T Wells, MSc > Myfyriwr PhD > Yr Ysgol Optometreg a Gwyddorau’r Golwg > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol > Seicoleg > Prifysgol Caerdydd > Heol Maindy > Caerdydd > CF24 4HQ > DU > > E-bost: wells...@caerdydd.ac.uk > Ffôn: 02920 879628 > > > On 17/04/2020, 15:32, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Bruce Fischl" fis...@nmr.mgh.harvard.edu> wrote: > > oh, then you probably want to use bbreg to register it and mri_vol2surf > to sample it onto the surface. Doug is the expert on this and can > add/correct if this is not the whole story :) > > cheers > Bruce > On Fri, 17 Apr 2020, Mason > Wells wrote: > > >External Email - Use Caution > > > > Hi Bruce, > > > > The only pre-processing I have done is the motion correction, high > pass filtering and distortion correction. So, as far as I know it is still in > the volume and in the original functional space. > > > > Best wishes, > > Mason > > > > Mason T Wells, MSc > > PhD student > > School of Optometry and Vision Sciences > > & Cardiff University Brain Research > > Imaging Centre (CUBRIC), School of Psychology > > Cardiff University > > Cardiff > > CF24 4HQ > > UK > > > > Email: wells...@cardiff.ac.uk > > Tel: 02920 879628 > > Web: Cardiff University webpage > <https://www.cardiff.ac.uk/people/research-students/view/974214-> > > Mason T Wells, MSc > > Myfyriwr PhD > > Yr Ysgol Optometreg a Gwyddorau’r Golwg > > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr > Ysgol Seicoleg > > Prifysgol Caerdydd > > Heol Maindy > > Caerdydd > > CF24 4HQ > > DU > > > > E-bost: wells...@caerdydd.ac.uk > > Ffôn: 02920 879628 > > > > > > On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on > behalf of Bruce Fischl" fis...@nmr.mgh.harvard.edu> wrote: > > > >Hi Mason > > > >is your filtered_func file already sampled onto the surface or is > it a > >volume? > > > >cheers > >Bruce > >On Fri, 17 Apr 2020, Mason Wells wrote: > > > >> > >> External Email - Use Caution > >> > >> Hi all, > >> > >> > >> > >> I am trying to use an analysis package that works on surface > based data > >> (SamSrf). I have ran Feat and have a filtered_func file which is > of course > >> the motion corrected/unwarped version of my EPI. However, I need > some advice > >> on how to get these data onto the Freesurfer surface. I have > found this > >> page, but I wanted to double check this is the most up-to-date > pipeline. On > >> the page it suggests using the same DOF as used in Feat, I use > BBR so this > >> seems a little redundant. Has anyone on these lists got any > experience of > >> getting filtered_func onto the Freesurfer surface? > >> > >> > >> > >> Thanks in advance, > >> > >> Mason > >> > >> > >> > >> > >> >
Re: [Freesurfer] Data on the Freesurfer surface
External Email - Use Caution
Great, thanks again Bruce.
Doug, can you confirm this is the process for taking a filtered_func file and
getting it onto the freesurfer surface ready for analysis?
Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK
Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU
E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628
On 17/04/2020, 15:32, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" wrote:
oh, then you probably want to use bbreg to register it and mri_vol2surf
to sample it onto the surface. Doug is the expert on this and can
add/correct if this is not the whole story :)
cheers
Bruce
On Fri, 17 Apr 2020, Mason
Wells wrote:
>External Email - Use Caution
>
> Hi Bruce,
>
> The only pre-processing I have done is the motion correction, high pass
filtering and distortion correction. So, as far as I know it is still in the
volume and in the original functional space.
>
> Best wishes,
> Mason
>
> Mason T Wells, MSc
> PhD student
> School of Optometry and Vision Sciences
> & Cardiff University Brain Research
> Imaging Centre (CUBRIC), School of Psychology
> Cardiff University
> Cardiff
> CF24 4HQ
> UK
>
> Email: wells...@cardiff.ac.uk
> Tel: 02920 879628
> Web: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->
> Mason T Wells, MSc
> Myfyriwr PhD
> Yr Ysgol Optometreg a Gwyddorau’r Golwg
> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr
Ysgol Seicoleg
> Prifysgol Caerdydd
> Heol Maindy
> Caerdydd
> CF24 4HQ
> DU
>
> E-bost: wells...@caerdydd.ac.uk
> Ffôn: 02920 879628
>
>
> On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of Bruce Fischl" wrote:
>
>Hi Mason
>
>is your filtered_func file already sampled onto the surface or is it a
>volume?
>
>cheers
>Bruce
>On Fri, 17 Apr 2020, Mason Wells wrote:
>
>>
>> External Email - Use Caution
>>
>> Hi all,
>>
>>
>>
>> I am trying to use an analysis package that works on surface based
data
>> (SamSrf). I have ran Feat and have a filtered_func file which is of
course
>> the motion corrected/unwarped version of my EPI. However, I need
some advice
>> on how to get these data onto the Freesurfer surface. I have found
this
>> page, but I wanted to double check this is the most up-to-date
pipeline. On
>> the page it suggests using the same DOF as used in Feat, I use BBR
so this
>> seems a little redundant. Has anyone on these lists got any
experience of
>> getting filtered_func onto the Freesurfer surface?
>>
>>
>>
>> Thanks in advance,
>>
>> Mason
>>
>>
>>
>>
>>
>> Mason T Wells, MSc
>>
>> PhD student
>>
>> School of Optometry and Vision Sciences
>>
>> & Cardiff University Brain Research
>>
>> Imaging Centre (CUBRIC), School of Psychology
>>
>> Cardiff University
>>
>> Cardiff
>>
>> CF24 4HQ
>>
>> UK
>>
>>
>>
>> Email: wells...@cardiff.ac.uk
>>
>> Tel: 02920 879628
>>
>> Web: Cardiff University webpage
>>
>> Mason T Wells, MSc
>>
>> Myfyriwr PhD
>>
>> Yr Ysgol Optometreg a Gwyddorau’r Golwg
>>
>> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC),
Yr Ysgol
>> Seicoleg
>>
>> Prifysgol Caerdydd
>>
>
Re: [Freesurfer] Data on the Freesurfer surface
oh, then you probably want to use bbreg to register it and mri_vol2surf to sample it onto the surface. Doug is the expert on this and can add/correct if this is not the whole story :) cheers Bruce On Fri, 17 Apr 2020, Mason Wells wrote: External Email - Use Caution Hi Bruce, The only pre-processing I have done is the motion correction, high pass filtering and distortion correction. So, as far as I know it is still in the volume and in the original functional space. Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: wells...@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: wells...@caerdydd.ac.uk Ffôn: 02920 879628 On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: Hi Mason is your filtered_func file already sampled onto the surface or is it a volume? cheers Bruce On Fri, 17 Apr 2020, Mason Wells wrote: > > External Email - Use Caution > > Hi all, > > > > I am trying to use an analysis package that works on surface based data > (SamSrf). I have ran Feat and have a filtered_func file which is of course > the motion corrected/unwarped version of my EPI. However, I need some advice > on how to get these data onto the Freesurfer surface. I have found this > page, but I wanted to double check this is the most up-to-date pipeline. On > the page it suggests using the same DOF as used in Feat, I use BBR so this > seems a little redundant. Has anyone on these lists got any experience of > getting filtered_func onto the Freesurfer surface? > > > > Thanks in advance, > > Mason > > > > > > Mason T Wells, MSc > > PhD student > > School of Optometry and Vision Sciences > > & Cardiff University Brain Research > > Imaging Centre (CUBRIC), School of Psychology > > Cardiff University > > Cardiff > > CF24 4HQ > > UK > > > > Email: wells...@cardiff.ac.uk > > Tel: 02920 879628 > > Web: Cardiff University webpage > > Mason T Wells, MSc > > Myfyriwr PhD > > Yr Ysgol Optometreg a Gwyddorau’r Golwg > > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol > Seicoleg > > Prifysgol Caerdydd > > Heol Maindy > > Caerdydd > > CF24 4HQ > > DU > > > > E-bost: wells...@caerdydd.ac.uk > > Ffôn: 02920 879628 > > > > > ___ 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
Re: [Freesurfer] Data on the Freesurfer surface
External Email - Use Caution Hi Bruce, The only pre-processing I have done is the motion correction, high pass filtering and distortion correction. So, as far as I know it is still in the volume and in the original functional space. Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: wells...@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: wells...@caerdydd.ac.uk Ffôn: 02920 879628 On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: Hi Mason is your filtered_func file already sampled onto the surface or is it a volume? cheers Bruce On Fri, 17 Apr 2020, Mason Wells wrote: > > External Email - Use Caution > > Hi all, > > > > I am trying to use an analysis package that works on surface based data > (SamSrf). I have ran Feat and have a filtered_func file which is of course > the motion corrected/unwarped version of my EPI. However, I need some advice > on how to get these data onto the Freesurfer surface. I have found this > page, but I wanted to double check this is the most up-to-date pipeline. On > the page it suggests using the same DOF as used in Feat, I use BBR so this > seems a little redundant. Has anyone on these lists got any experience of > getting filtered_func onto the Freesurfer surface? > > > > Thanks in advance, > > Mason > > > > > > Mason T Wells, MSc > > PhD student > > School of Optometry and Vision Sciences > > & Cardiff University Brain Research > > Imaging Centre (CUBRIC), School of Psychology > > Cardiff University > > Cardiff > > CF24 4HQ > > UK > > > > Email: wells...@cardiff.ac.uk > > Tel: 02920 879628 > > Web: Cardiff University webpage > > Mason T Wells, MSc > > Myfyriwr PhD > > Yr Ysgol Optometreg a Gwyddorau’r Golwg > > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol > Seicoleg > > Prifysgol Caerdydd > > Heol Maindy > > Caerdydd > > CF24 4HQ > > DU > > > > E-bost: wells...@caerdydd.ac.uk > > Ffôn: 02920 879628 > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Data on the Freesurfer surface
Hi Mason is your filtered_func file already sampled onto the surface or is it a volume? cheers Bruce On Fri, 17 Apr 2020, Mason Wells wrote: External Email - Use Caution Hi all, I am trying to use an analysis package that works on surface based data (SamSrf). I have ran Feat and have a filtered_func file which is of course the motion corrected/unwarped version of my EPI. However, I need some advice on how to get these data onto the Freesurfer surface. I have found this page, but I wanted to double check this is the most up-to-date pipeline. On the page it suggests using the same DOF as used in Feat, I use BBR so this seems a little redundant. Has anyone on these lists got any experience of getting filtered_func onto the Freesurfer surface? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: wells...@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: wells...@caerdydd.ac.uk Ffôn: 02920 879628 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Data on the Freesurfer surface
External Email - Use Caution Hi all, I am trying to use an analysis package that works on surface based data (SamSrf). I have ran Feat and have a filtered_func file which is of course the motion corrected/unwarped version of my EPI. However, I need some advice on how to get these data onto the Freesurfer surface. I have found this page<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer>, but I wanted to double check this is the most up-to-date pipeline. On the page it suggests using the same DOF as used in Feat, I use BBR so this seems a little redundant. Has anyone on these lists got any experience of getting filtered_func onto the Freesurfer surface? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk> Ffôn: 02920 879628 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Data onto the Freesurfer surface
External Email - Use Caution Hi all, I apologise for cross-posting to both FSL and Freesurfer lists. I am trying to use an analysis package that works on surface based data (SamSrf). I have ran Feat and have a filtered_func file which is of course the motion corrected/unwarped version of my EPI. However, I need some advice on how to get these data onto the Freesurfer surface. I have found this page<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer>, but I wanted to double check this is the most up-to-date pipeline. On the page it suggests using the same DOF as used in Feat, I use BBR so this seems a little redundant. Has anyone on these lists got any experience of getting filtered_func onto the Freesurfer surface? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk> Ffôn: 02920 879628 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
