Sorry to bug again with this issue when converting the freesurfer surface to GIFTI using mris_convert the surface is shifted in space. Does anyone know how to transform it to freesurfer space?
Thanks! Shani
On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi saad@fmrib.ox.ac.uk wrote:
You need to convert your surface file into a format that workbench understand (GIFTI):
mris_convert lh.whiteinraw lh.whiteinraw.surf.gii
Cheers Saad
On 3 Sep 2013, at 10:57, Shani Ben Amitay shani.holzer@gmail.com wrote:
Thank you! Still somehow I haven't manage to make it work when I ran the suggested command I get an error saying : ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error occurred while parsing element line number: 1 column number: 1. Any advise?
Thanks again
Shani
On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote:
Hi Bruce,
Connectome Workbench commandline utilities can do this with FSL warp fields:
wb_command -surface-apply-warpfield
One needs to use the inverse warp as the <warpfield> argument and the forward warp as the -fnirt <forward-warp>.
Peace,
Matt.
On 9/2/13 11:19 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
A veritable game of telephone! Thanks Jesper. Matt?
On Mon, 2 Sep 2013, Jesper Andersson wrote:
Hi guys, I didn't think we had any tools for doing that, and said so much on
the
FSL mailbase. But apparently the WashU people has something that does just that for you. I think the best person to contact about the details is Matt Glasser.
J
On 2 Sep 2013, at 15:58, Saad Jbabdi saad@FMRIB.OX.AC.UK wrote:
Hi In Probtrackx, this is done internally.If you just want to transform the vertex coordinates, then I think you'll need to play with the FNIRT source code - I've CC'd Jesper who knows better.
Cheers, Saad
On 2 Sep 2013, at 15:56, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
you might check on the FSL list. I think I've seen some traffic indicating that there are some tools for doing this. I'l cc Saad as he might know cheers Bruce On Mon, 2 Sep 2013, Douglas Greve wrote: Hi Shani, I don't think you can apply a FNIRT transform to a surface. doug On 9/2/13 8:20 AM, Shani Ben Amitay wrote: Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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.-- Saad Jbabdi University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Saad Jbabdi University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
Hi Shani
how do you know it is shifted?
Bruce
On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
Sorry to bug again with this issue when converting the freesurfer surface to GIFTI using mris_convert the surface is shifted in space. Does anyone know how to transform it to freesurfer space?
Thanks! Shani
On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi saad@fmrib.ox.ac.uk wrote: You need to convert your surface file into a format that workbench understand (GIFTI): mris_convert lh.whiteinraw lh.whiteinraw.surf.gii
Cheers Saad
On 3 Sep 2013, at 10:57, Shani Ben Amitay shani.holzer@gmail.com wrote:
Thank you!Still somehow I haven't manage to make it work when I ran the suggested command I get an error saying :ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error occurred while parsing element line number: 1 column number: 1. Any advise?
Thanks again
Shani
On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote:
> Hi Bruce, > > Connectome Workbench commandline utilities can do this with FSL warp > fields: > > wb_command -surface-apply-warpfield > > One needs to use the inverse warp as the <warpfield> argument and the > forward warp as the -fnirt <forward-warp>. > > Peace, > > Matt. > > On 9/2/13 11:19 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: > >> A veritable game of telephone! Thanks Jesper. Matt? >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >>> Hi guys, >>> I didn't think we had any tools for doing that, and said so much on the >>> FSL >>> mailbase. But apparently the WashU people has something that does just >>> that >>> for you. I think the best person to contact about the details is Matt >>> Glasser. >>> >>> J >>> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad@FMRIB.OX.AC.UK> >>> wrote: >>> >>> Hi In Probtrackx, this is done internally. >>> If you just want to transform the vertex coordinates, then I think >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >>> knows better. >>> >>> Cheers, >>> Saad >>> >>> >>> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl@nmr.mgh.harvard.edu> >>> wrote: >>> >>> you might check on the FSL list. I think I've seen some >>> traffic indicating that there are some tools for doing >>> this. I'l cc Saad as he might know >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >>> >>> Hi Shani, I don't think you can apply a FNIRT >>> transform to a surface. >>> doug >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >>> Dear freesurfer people, >>> Any idea whether I can apply transformation >>> that was calculated by fsl >>> fnirt on the white/pial surfaces calculated >>> using the freesurfer >>> stream? >>> Thanks! >>> Shani >>> _______________________________________________ >>> 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. >>> >>> >>> >>> -- >>> Saad Jbabdi >>> University of Oxford, FMRIB Centre >>> >>> JR Hospital, Headington, OX3 9DU, UK >>> (+44)1865-222466 (fax 717) >>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi >>> >>> >>> > > > ________________________________The materials in this message are private and may
contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Saad Jbabdi University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
Im looking at the gifti and fs surfaces in freeview they are not aligned.this surface was reconstructed with noaparc and noaseg.maybe transformation file is missing? thank you shani בתאריך 8 בספט 2013 16:59, מאת "Bruce Fischl" fischl@nmr.mgh.harvard.edu:
Hi Shani
how do you know it is shifted?
Bruce
On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
Sorry to bug again with this issue when converting the freesurfer surface
to GIFTI using mris_convert the surface is shifted in space. Does anyone know how to transform it to freesurfer space?
Thanks! Shani
On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi saad@fmrib.ox.ac.uk wrote: You need to convert your surface file into a format that workbench understand (GIFTI): mris_convert lh.whiteinraw lh.**whiteinraw.surf.gii
Cheers Saad
On 3 Sep 2013, at 10:57, Shani Ben Amitay shani.holzer@gmail.com wrote:
Thank you!Still somehow I haven't manage to make it work when I ran the suggested command I get an error saying :ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error occurred while parsing element line number: 1 column number: 1. Any advise?
Thanks again
Shani
On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote:
> Hi Bruce, > > Connectome Workbench commandline utilities can do this with FSL warp > fields: > > wb_command -surface-apply-warpfield > > One needs to use the inverse warp as the <warpfield> argument and the > forward warp as the -fnirt <forward-warp>. > > Peace, > > Matt. > > On 9/2/13 11:19 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: > >> A veritable game of telephone! Thanks Jesper. Matt? >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >>> Hi guys, >>> I didn't think we had any tools for doing that, and said so much on the >>> FSL >>> mailbase. But apparently the WashU people has something that does just >>> that >>> for you. I think the best person to contact about the details is Matt >>> Glasser. >>> >>> J >>> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad@FMRIB.OX.AC.UK> >>> wrote: >>> >>> Hi In Probtrackx, this is done internally. >>> If you just want to transform the vertex coordinates, then I think >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >>> knows better. >>> >>> Cheers, >>> Saad >>> >>> >>> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl@nmr.mgh.harvard.edu> >>> wrote: >>> >>> you might check on the FSL list. I think I've seen some >>> traffic indicating that there are some tools for doing >>> this. I'l cc Saad as he might know >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >>> >>> Hi Shani, I don't think you can apply a FNIRT >>> transform to a surface. >>> doug >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >>> Dear freesurfer people, >>> Any idea whether I can apply transformation >>> that was calculated by fsl >>> fnirt on the white/pial surfaces calculated >>> using the freesurfer >>> stream? >>> Thanks! >>> Shani >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >>> >>> >>> >>> -- >>> Saad Jbabdi >>> University of Oxford, FMRIB Centre >>> >>> JR Hospital, Headington, OX3 9DU, UK >>> (+44)1865-222466 (fax 717) >>> www.ndcn.ox.ac.uk/team/**researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi> >>> >>> >>> > > > ______________________________**__The materials in this message are private and may
contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Saad Jbabdi University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/**researchers/saad-jbabdihttp://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
so you run recon-all, convert to gifti and display that and it doesn't match the original surface? On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
Im looking at the gifti and fs surfaces in freeview they are not aligned.this surface was reconstructed with noaparc and noaseg.maybe transformation file is missing? thank you shani
בתאריך 8 בספט 2013 16:59, מאת "Bruce Fischl" fischl@nmr.mgh.harvard.edu: Hi Shani
how do you know it is shifted? Bruce On Sun, 8 Sep 2013, Shani Ben Amitay wrote: Sorry to bug again with this issue when converting the freesurfer surface to GIFTI using mris_convert the surface is shifted in space. Does anyone know how to transform it to freesurfer space? Thanks! Shani On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi <saad@fmrib.ox.ac.uk> wrote: You need to convert your surface file into a format that workbench understand (GIFTI): mris_convert lh.whiteinraw lh.whiteinraw.surf.gii Cheers Saad On 3 Sep 2013, at 10:57, Shani Ben Amitay <shani.holzer@gmail.com> wrote: Thank you!Still somehow I haven't manage to make it work when I ran the suggested command I get an error saying : ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error occurred while parsing element line number: 1 column number: 1. Any advise? Thanks again Shani On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote: > Hi Bruce, > > Connectome Workbench commandline utilities can do this with FSL warp > fields: > > wb_command -surface-apply-warpfield > > One needs to use the inverse warp as the <warpfield> argument and the > forward warp as the -fnirt <forward-warp>. > > Peace, > > Matt. > > On 9/2/13 11:19 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: > >> A veritable game of telephone! Thanks Jesper. Matt? >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >>> Hi guys, >>> I didn't think we had any tools for doing that, and said so much on the >>> FSL >>> mailbase. But apparently the WashU people has something that does just >>> that >>> for you. I think the best person to contact about the details is Matt >>> Glasser. >>> >>> J >>> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad@FMRIB.OX.AC.UK> >>> wrote: >>> >>> Hi In Probtrackx, this is done internally. >>> If you just want to transform the vertex coordinates, then I think >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >>> knows better. >>> >>> Cheers, >>> Saad >>> >>> >>> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl@nmr.mgh.harvard.edu> >>> wrote: >>> >>> you might check on the FSL list. I think I've seen some >>> traffic indicating that there are some tools for doing >>> this. I'l cc Saad as he might know >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >>> >>> Hi Shani, I don't think you can apply a FNIRT >>> transform to a surface. >>> doug >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >>> Dear freesurfer people, >>> Any idea whether I can apply transformation >>> that was calculated by fsl >>> fnirt on the white/pial surfaces calculated >>> using the freesurfer >>> stream? >>> Thanks! >>> Shani >>> _______________________________________________ >>> 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. >>> >>> >>> >>> -- >>> Saad Jbabdi >>> University of Oxford, FMRIB Centre >>> >>> JR Hospital, Headington, OX3 9DU, UK >>> (+44)1865-222466 (fax 717) >>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi >>> >>> >>> > > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
'm running the following commands to reconstruct the white and pial surfaces(non-human data)
mri_pretess mri/filled/filled.mgz 255 mri/brain.mgz mri/filled-pretess255.mgz mri_tessellate mri/filled-pretess255.mgz 255 surf/lh.orig.nofix mris_extract_main_component surf/lh.orig.nofix surf/lh.orig.nofix mris_smooth -nw surf/lh.orig.nofix surf/lh.smoothwm.nofix mris_inflate -no-save-sulc surf/lh.smoothwm.nofix surf/lh.inflated.nofix mris_make_surfaces -noaparc -noaseg -mgz -T1 brain rat1 lh -pial
Thank you Shani
On Sun, Sep 8, 2013 at 6:37 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
so you run recon-all, convert to gifti and display that and it doesn't match the original surface?
On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
Im looking at the gifti and fs surfaces in freeview they are not aligned.this surface was reconstructed with noaparc and noaseg.maybe transformation file is missing? thank you shani
בתאריך 8 בספט 2013 16:59, מאת "Bruce Fischl" <fischl@nmr.mgh.harvard.edu
:
Hi Shani how do you know it is shifted? Bruce On Sun, 8 Sep 2013, Shani Ben Amitay wrote: Sorry to bug again with this issue when converting the freesurfer surface to GIFTI using mris_convert the surface is shifted in space. Does anyone know how to transform it to freesurfer space? Thanks! Shani On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi <saad@fmrib.ox.ac.uk> wrote: You need to convert your surface file into a format that workbench understand (GIFTI): mris_convert lh.whiteinraw lh.**whiteinraw.surf.gii Cheers Saad On 3 Sep 2013, at 10:57, Shani Ben Amitay <shani.holzer@gmail.com> wrote: Thank you!Still somehow I haven't manage to make it work when I ran the suggested command I get an error saying : ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error occurred while parsing element line number: 1 column number: 1. Any advise? Thanks again Shani On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote: > Hi Bruce, > > Connectome Workbench commandline utilities can do this with FSL warp > fields: > > wb_command -surface-apply-warpfield > > One needs to use the inverse warp as the <warpfield> argument and the > forward warp as the -fnirt <forward-warp>. > > Peace, > > Matt. > > On 9/2/13 11:19 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: > >> A veritable game of telephone! Thanks Jesper. Matt? >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >>> Hi guys, >>> I didn't think we had any tools for doing that, and said so much on the >>> FSL >>> mailbase. But apparently the WashU people has something that does just >>> that >>> for you. I think the best person to contact about the details is Matt >>> Glasser. >>> >>> J >>> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad@FMRIB.OX.AC.UK> >>> wrote: >>> >>> Hi In Probtrackx, this is done internally. >>> If you just want to transform the vertex coordinates, then I think >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >>> knows better. >>> >>> Cheers, >>> Saad >>> >>> >>> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl@nmr.mgh.harvard.edu> >>> wrote: >>> >>> you might check on the FSL list. I think I've seen some >>> traffic indicating that there are some tools for doing >>> this. I'l cc Saad as he might know >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >>> >>> Hi Shani, I don't think you can apply a FNIRT >>> transform to a surface. >>> doug >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >>> Dear freesurfer people, >>> Any idea whether I can apply transformation >>> that was calculated by fsl >>> fnirt on the white/pial surfaces calculated >>> using the freesurfer >>> stream? >>> Thanks! >>> Shani >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer 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/**compliancelinehttp://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. >>> >>> >>> >>> -- >>> Saad Jbabdi >>> University of Oxford, FMRIB Centre >>> >>> JR Hospital, Headington, OX3 9DU, UK >>> (+44)1865-222466 (fax 717) >>> www.ndcn.ox.ac.uk/team/**researchers/saad-jbabdihttp://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi >>> >>> >>> > > > ______________________________**__ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > > ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/**researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi>
Hi Shani,
then what? How do you convert to gifti? And does that surface look differently before and after conversion in freeview? Bruce On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
'm running the following commands to reconstruct the white and pial surfaces(non-human data) mri_pretess mri/filled/filled.mgz 255 mri/brain.mgz mri/filled-pretess255.m gz mri_tessellate mri/filled-pretess255.mgz 255 surf/lh.orig.nofix mris_extract_main_component surf/lh.orig.nofix surf/lh.orig.nofix mris_smooth -nw surf/lh.orig.nofix surf/lh.smoothwm.nofix mris_inflate -no-save-sulc surf/lh.smoothwm.nofix surf/lh.inflated.nofix mris_make_surfaces -noaparc -noaseg -mgz -T1 brain rat1 lh -pial
Thank you Shani [cleardot.gif]
On Sun, Sep 8, 2013 at 6:37 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: so you run recon-all, convert to gifti and display that and it doesn't match the original surface? On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
Im looking at the gifti and fs surfaces in freeview they are not aligned.this surface was reconstructed with noaparc and noaseg.maybe transformation file is missing? thank you shani בתאריך 8 בספט 2013 16:59, מאת "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>: Hi Shani how do you know it is shifted? Bruce On Sun, 8 Sep 2013, Shani Ben Amitay wrote: Sorry to bug again with this issue when converting the freesurfer surface to GIFTI using mris_convert the surface is shifted in space. Does anyone know how to transform it to freesurfer space? Thanks! Shani On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi <saad@fmrib.ox.ac.uk> wrote: You need to convert your surface file into a format that workbench understand (GIFTI): mris_convert lh.whiteinraw lh.whiteinraw.surf.gii Cheers Saad On 3 Sep 2013, at 10:57, Shani Ben Amitay <shani.holzer@gmail.com> wrote: Thank you!Still somehow I haven't manage to make it work when I ran the suggested command I get an error saying : ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error occurred while parsing element line number: 1 column number: 1. Any advise? Thanks again Shani On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote: > Hi Bruce, > > Connectome Workbench commandline utilities can do this with FSL warp > fields: > > wb_command -surface-apply-warpfield > > One needs to use the inverse warp as the <warpfield> argument and the > forward warp as the -fnirt <forward-warp>. > > Peace, > > Matt. > > On 9/2/13 11:19 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: > >> A veritable game of telephone! Thanks Jesper. Matt? >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >>> Hi guys, >>> I didn't think we had any tools for doing that, and said so much on the >>> FSL >>> mailbase. But apparently the WashU people has something that does just >>> that >>> for you. I think the best person to contact about the details is Matt >>> Glasser. >>> >>> J >>> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad@FMRIB.OX.AC.UK> >>> wrote: >>> >>> Hi In Probtrackx, this is done internally. >>> If you just want to transform the vertex coordinates, then I think >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >>> knows better. >>> >>> Cheers, >>> Saad >>> >>> >>> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl@nmr.mgh.harvard.edu> >>> wrote: >>> >>> you might check on the FSL list. I think I've seen some >>> traffic indicating that there are some tools for doing >>> this. I'l cc Saad as he might know >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >>> >>> Hi Shani, I don't think you can apply a FNIRT >>> transform to a surface. >>> doug >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >>> Dear freesurfer people, >>> Any idea whether I can apply transformation >>> that was calculated by fsl >>> fnirt on the white/pial surfaces calculated >>> using the freesurfer >>> stream? >>> Thanks! >>> Shani >>> _______________________________________________ >>> 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. >>> >>> >>> >>> -- >>> Saad Jbabdi >>> University of Oxford, FMRIB Centre >>> >>> JR Hospital, Headington, OX3 9DU, UK >>> (+44)1865-222466 (fax 717) >>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi >>> >>> >>> > > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
Hi,
I convert it using mris_convert lh.white lh.white.gii the surface looks the same but shifted (see attached)
Thanks [image: Inline image 1]
On Sun, Sep 8, 2013 at 11:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Shani,
then what? How do you convert to gifti? And does that surface look differently before and after conversion in freeview?
Bruce On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
'm running the following commands to reconstruct the white and pial
surfaces(non-human data) mri_pretess mri/filled/filled.**mgz 255 mri/brain.mgz mri/** filled-pretess255.m gz mri_tessellate mri/filled-**pretess255.mgz 255 surf/lh.orig.nofix mris_extract_main_component surf/lh.orig.nofix surf/lh.**orig.nofix mris_smooth -nw surf/lh.orig.nofix surf/**lh.smoothwm.nofix mris_inflate -no-save-sulc surf/lh.**smoothwm.nofix surf/lh.** inflated.nofix mris_make_surfaces -noaparc -noaseg -mgz -T1 brain rat1 lh -pial
Thank you Shani [cleardot.gif]
On Sun, Sep 8, 2013 at 6:37 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: so you run recon-all, convert to gifti and display that and it doesn't match the original surface? On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
Im looking at the gifti and fs surfaces in freeview they are not aligned.this surface was reconstructed with noaparc and noaseg.maybe transformation file is missing? thank you shani בתאריך 8 בספט 2013 16:59, מאת "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>: Hi Shani how do you know it is shifted? Bruce On Sun, 8 Sep 2013, Shani Ben Amitay wrote: Sorry to bug again with this issue when converting the freesurfer surface to GIFTI using mris_convert the surface is shifted in space. Does anyone know how to transform it to freesurfer space? Thanks! Shani On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi <saad@fmrib.ox.ac.uk> wrote: You need to convert your surface file into a format that workbench understand (GIFTI): mris_convert lh.whiteinraw lh.**whiteinraw.surf.gii Cheers Saad On 3 Sep 2013, at 10:57, Shani Ben Amitay <shani.holzer@gmail.com> wrote: Thank you!Still somehow I haven't manage to make it work when I ran the suggested command I get an error saying : ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error occurred while parsing element line number: 1 column number: 1. Any advise? Thanks again Shani On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote: > Hi Bruce, > > Connectome Workbench commandline utilities can do this with FSL warp > fields: > > wb_command -surface-apply-warpfield > > One needs to use the inverse warp as the <warpfield> argument and the > forward warp as the -fnirt <forward-warp>. > > Peace, > > Matt. > > On 9/2/13 11:19 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: > >> A veritable game of telephone! Thanks Jesper. Matt? >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >>> Hi guys, >>> I didn't think we had any tools for doing that, and said so much on the >>> FSL >>> mailbase. But apparently the WashU people has something that does just >>> that >>> for you. I think the best person to contact about the details is Matt >>> Glasser. >>> >>> J >>> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad@FMRIB.OX.AC.UK> >>> wrote: >>> >>> Hi In Probtrackx, this is done internally. >>> If you just want to transform the vertex coordinates, then I think >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >>> knows better. >>> >>> Cheers, >>> Saad >>> >>> >>> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl@nmr.mgh.harvard.edu> >>> wrote: >>> >>> you might check on the FSL list. I think I've seen some >>> traffic indicating that there are some tools for doing >>> this. I'l cc Saad as he might know >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >>> >>> Hi Shani, I don't think you can apply a FNIRT >>> transform to a surface. >>> doug >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >>> Dear freesurfer people, >>> Any idea whether I can apply transformation >>> that was calculated by fsl >>> fnirt on the white/pial surfaces calculated >>> using the freesurfer >>> stream? >>> Thanks! >>> Shani >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer 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/**compliancelinehttp://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. >>> >>> >>> >>> -- >>> Saad Jbabdi >>> University of Oxford, FMRIB Centre >>> >>> JR Hospital, Headington, OX3 9DU, UK >>> (+44)1865-222466 (fax 717) >>>
www.ndcn.ox.ac.uk/team/**researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi> >>> >>> >>> > > > ______________________________**__ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > > ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/**researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi>
Problem solved-I've managed to do it using -t subject_id Thanks, Shani
On Mon, Sep 9, 2013 at 8:44 AM, Shani Ben Amitay shani.holzer@gmail.comwrote:
Hi,
I convert it using mris_convert lh.white lh.white.gii the surface looks the same but shifted (see attached)
Thanks [image: Inline image 1]
On Sun, Sep 8, 2013 at 11:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Shani,
then what? How do you convert to gifti? And does that surface look differently before and after conversion in freeview?
Bruce On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
'm running the following commands to reconstruct the white and pial
surfaces(non-human data) mri_pretess mri/filled/filled.**mgz 255 mri/brain.mgz mri/** filled-pretess255.m gz mri_tessellate mri/filled-**pretess255.mgz 255 surf/lh.orig.nofix mris_extract_main_component surf/lh.orig.nofix surf/lh.**orig.nofix mris_smooth -nw surf/lh.orig.nofix surf/**lh.smoothwm.nofix mris_inflate -no-save-sulc surf/lh.**smoothwm.nofix surf/lh.** inflated.nofix mris_make_surfaces -noaparc -noaseg -mgz -T1 brain rat1 lh -pial
Thank you Shani [cleardot.gif]
On Sun, Sep 8, 2013 at 6:37 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: so you run recon-all, convert to gifti and display that and it doesn't match the original surface? On Sun, 8 Sep 2013, Shani Ben Amitay wrote:
Im looking at the gifti and fs surfaces in freeview they are not aligned.this surface was reconstructed with noaparc and noaseg.maybe transformation file is missing? thank you shani בתאריך 8 בספט 2013 16:59, מאת "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>: Hi Shani how do you know it is shifted? Bruce On Sun, 8 Sep 2013, Shani Ben Amitay wrote: Sorry to bug again with this issue when converting the freesurfer surface to GIFTI using mris_convert the surface is shifted in space. Does anyone know how to transform it to freesurfer space? Thanks! Shani On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi <saad@fmrib.ox.ac.uk> wrote: You need to convert your surface file into a format that workbench understand (GIFTI): mris_convert lh.whiteinraw lh.**whiteinraw.surf.gii Cheers Saad On 3 Sep 2013, at 10:57, Shani Ben Amitay <shani.holzer@gmail.com> wrote: Thank you!Still somehow I haven't manage to make it work when I ran the suggested command I get an error saying : ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error occurred while parsing element line number: 1 column number: 1. Any advise? Thanks again Shani On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote: > Hi Bruce, > > Connectome Workbench commandline utilities can do this with FSL warp > fields: > > wb_command -surface-apply-warpfield > > One needs to use the inverse warp as the <warpfield> argument and the > forward warp as the -fnirt <forward-warp>. > > Peace, > > Matt. > > On 9/2/13 11:19 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: > >> A veritable game of telephone! Thanks Jesper. Matt? >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >>> Hi guys, >>> I didn't think we had any tools for doing that, and said so much on the >>> FSL >>> mailbase. But apparently the WashU people has something that does just >>> that >>> for you. I think the best person to contact about the details is Matt >>> Glasser. >>> >>> J >>> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad@FMRIB.OX.AC.UK> >>> wrote: >>> >>> Hi In Probtrackx, this is done internally. >>> If you just want to transform the vertex coordinates, then I think >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >>> knows better. >>> >>> Cheers, >>> Saad >>> >>> >>> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl@nmr.mgh.harvard.edu> >>> wrote: >>> >>> you might check on the FSL list. I think I've seen some >>> traffic indicating that there are some tools for doing >>> this. I'l cc Saad as he might know >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >>> >>> Hi Shani, I don't think you can apply a FNIRT >>> transform to a surface. >>> doug >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >>> Dear freesurfer people, >>> Any idea whether I can apply transformation >>> that was calculated by fsl >>> fnirt on the white/pial surfaces calculated >>> using the freesurfer >>> stream? >>> Thanks! >>> Shani >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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. >>> >>> >>> >>> -- >>> Saad Jbabdi >>> University of Oxford, FMRIB Centre >>> >>> JR Hospital, Headington, OX3 9DU, UK >>> (+44)1865-222466 (fax 717) >>>
www.ndcn.ox.ac.uk/team/**researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi> >>> >>> >>> > > > ______________________________**__ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > > ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/**researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi>
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Shani Ben Amitay