Dear Bruce If I want to rotate sucli pattern too if it is the same?
On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
I guess you could rotate the surfaces, save them, then resample the labels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this.
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce
I think the easiest way is to create all surfaces again but with corrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?!
Bests Rouhi
On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files. On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: not easily. Why would you need to do such a thing? On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set? Best Rouhi On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Rouhi I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem. cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: Dear Bruce I am working on Freesurfer 2 caret meshes. I am using **FreeSurfer2CaretConvertAndRegi**sterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created? Thank you very much Rouhi On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Try using fsaverage as the trgsubject Cheers Bruce On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage 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. -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi-- With Best Regards Rouhollah Abdollahi
I tried to rotate the surface by tksurfer and save it as new file . But when I open the new surface like white it was not rotated. Is there any special thing that I have to do?
Best Rouhi
On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi roohy466@gmail.comwrote:
Dear Bruce If I want to rotate sucli pattern too if it is the same?
On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
I guess you could rotate the surfaces, save them, then resample the labels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this.
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce
I think the easiest way is to create all surfaces again but with corrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?!
Bests Rouhi
On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files. On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: not easily. Why would you need to do such a thing? On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set? Best Rouhi On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Rouhi I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem. cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: Dear Bruce I am working on Freesurfer 2 caret meshes. I am using **FreeSurfer2CaretConvertAndRegi**sterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created? Thank you very much Rouhi On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Try using fsaverage as the trgsubject Cheers Bruce On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage 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. -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
So I thought the issue had been solved, but perhaps not. Bruce, we (i.e. David) think the problem with Rouhi's data is that FreeSurfer did not detect that the original images were tipped forward 90 degrees and as a result the surface registration failed intermittently (i.e. in some subjects it okay, but in others it is not). These data were created with a fairly old version of FreeSurfer (Rouhi can give the version number), and then a significant amount of manual effort was put into defining some retinotopy on the data. Therefore it isn't really a feasible option to just rerun the data with a newer version of FreeSurfer, but we want to make use of accurate FreeSurfer surface registration to make group average retinotopy results. So the question is how do we go about making sure the spheres are initialized to have the correct rigid orientation before the registration proceeds.
Thanks,
Matt.
_____
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi Sent: Friday, August 12, 2011 12:38 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Label2label on fsaverage
I tried to rotate the surface by tksurfer and save it as new file . But when I open the new surface like white it was not rotated. Is there any special thing that I have to do?
Best Rouhi
On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi roohy466@gmail.com wrote:
Dear Bruce If I want to rotate sucli pattern too if it is the same?
On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I guess you could rotate the surfaces, save them, then resample the labels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this.
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce I think the easiest way is to create all surfaces again but with corrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?!
Bests Rouhi
On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files.
On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: not easily. Why would you need to do such a thing?
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce
I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set?
Best Rouhi
On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Rouhi
I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem.
cheers Bruce
On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem.
Thanks for your quick response.
On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi roohy466@gmail.com wrote: Dear Bruce
I am working on Freesurfer 2 caret meshes. I am using FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created?
Thank you very much
Rouhi
On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Try using fsaverage as the trgsubject Cheers Bruce
On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi roohy466@gmail.com wrote:
> .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage
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.
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
Hi Matt
if they were tipped forward 90deg and we didn't detect it I would think that the aseg would fail catastrophically. Did that happen? Bruce On Fri, 12 Aug 2011, Matt Glasser wrote:
So I thought the issue had been solved, but perhaps not. Bruce, we (i.e. David) think the problem with Rouhi?s data is that FreeSurfer did not detect that the original images were tipped forward 90 degrees and as a result the surface registration failed intermittently (i.e. in some subjects it okay, but in others it is not). These data were created with a fairly old version of FreeSurfer (Rouhi can give the version number), and then a significant amount of manual effort was put into defining some retinotopy on the data. Therefore it isn?t really a feasible option to just rerun the data with a newer version of FreeSurfer, but we want to make use of accurate FreeSurfer surface registration to make group average retinotopy results. So the question is how do we go about making sure the spheres are initialized to have the correct rigid orientation before the registration proceeds.
Thanks,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi Sent: Friday, August 12, 2011 12:38 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Label2label on fsaverage
I tried to rotate the surface by tksurfer and save it as new file . But when I open the new surface like white it was not rotated. Is there any special thing that I have to do?
Best Rouhi
On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi roohy466@gmail.com wrote:
Dear Bruce If I want to rotate sucli pattern too if it is the same?
On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I guess you could rotate the surfaces, save them, then resample the labels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this.
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce I think the easiest way is to create all surfaces again but with corrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?!
Bests Rouhi
On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files.
On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: not easily. Why would you need to do such a thing?
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce
I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set?
Best Rouhi
On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Rouhi
I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem.
cheers Bruce
On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem.
Thanks for your quick response.
On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi roohy466@gmail.com wrote: Dear Bruce
I am working on Freesurfer 2 caret meshes. I am using FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created?
Thank you very much
Rouhi
On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Try using fsaverage as the trgsubject Cheers Bruce
On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi roohy466@gmail.com wrote:
> .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage
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.
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
--
With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
Hi Bruce I think the aseg is good but only rotated 90 degree. I will try to rotate sphere to see how it will create sphere.reg.
On Sat, Aug 13, 2011 at 1:02 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Matt
if they were tipped forward 90deg and we didn't detect it I would think that the aseg would fail catastrophically. Did that happen? Bruce
On Fri, 12 Aug 2011, Matt Glasser wrote:
So I thought the issue had been solved, but perhaps not. Bruce, we (i.e. David) think the problem with Rouhi?s data is that FreeSurfer did not detect that the original images were tipped forward 90 degrees and as a result the surface registration failed intermittently (i.e. in some subjects it okay, but in others it is not). These data were created with a fairly old version of FreeSurfer (Rouhi can give the version number), and then a significant amount of manual effort was put into defining some retinotopy on the data. Therefore it isn?t really a feasible option to just rerun the data with a newer version of FreeSurfer, but we want to make use of accurate FreeSurfer surface registration to make group average retinotopy results. So the question is how do we go about making sure the spheres are initialized to have the correct rigid orientation before the registration proceeds.
Thanks,
Matt.
______________________________**______________________________** ______________________________**______________________________** _________________________
From: freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu[mailto: freesurfer-bounces@**nmr.mgh.harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi Sent: Friday, August 12, 2011 12:38 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Label2label on fsaverage
I tried to rotate the surface by tksurfer and save it as new file . But when I open the new surface like white it was not rotated. Is there any special thing that I have to do?
Best Rouhi
On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi roohy466@gmail.com wrote:
Dear Bruce If I want to rotate sucli pattern too if it is the same?
On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I guess you could rotate the surfaces, save them, then resample the labels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this.
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce I think the easiest way is to create all surfaces again but with corrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?!
Bests Rouhi
On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files. On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: not easily. Why would you need to do such a thing? On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set? Best Rouhi On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Rouhi I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem. cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: Dear Bruce I am working on Freesurfer 2 caret meshes. I am using **FreeSurfer2CaretConvertAndRegi**sterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created? Thank you very much Rouhi On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Try using fsaverage as the trgsubject Cheers Bruce On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --**0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage 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. -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi-- With Best Regards Rouhollah Abdollahi
--
With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
if the aseg is good I don't see how it's possible that we don't know about the 90 deg rotation. If you upload the dataset I'll take a look On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote:
Hi BruceI think the aseg is good but only rotated 90 degree. I will try to rotate sphere to see how it will create sphere.reg.
On Sat, Aug 13, 2011 at 1:02 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Matt
if they were tipped forward 90deg and we didn't detect it I would think that the aseg would fail catastrophically. Did that happen? BruceOn Fri, 12 Aug 2011, Matt Glasser wrote:
So I thought the issue had been solved, but perhaps not. Bruce, we (i.e. David) think the problem with Rouhi?s data is that FreeSurfer did not detect that the original images were tipped forward 90 degrees and as a result the surface registration failed intermittently (i.e. in some subjects it okay, but in others it is not). These data were created with a fairly old version of FreeSurfer (Rouhi can give the version number), and then a significant amount of manual effort was put into defining some retinotopy on the data. Therefore it isn?t really a feasible option to just rerun the data with a newer version of FreeSurfer, but we want to make use of accurate FreeSurfer surface registration to make group average retinotopy results. So the question is how do we go about making sure the spheres are initialized to have the correct rigid orientation before the registration proceeds. Thanks, Matt. _________________________________________________________________________________________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi Sent: Friday, August 12, 2011 12:38 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Label2label on fsaverage I tried to rotate the surface by tksurfer and save it as new file . But when I open the new surface like white it was not rotated. Is there any special thing that I have to do? Best Rouhi On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: Dear Bruce If I want to rotate sucli pattern too if it is the same? On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: I guess you could rotate the surfaces, save them, then resample the labels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this. On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think the easiest way is to create all surfaces again but with corrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?! Bests Rouhi On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files. On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: not easily. Why would you need to do such a thing? On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set? Best Rouhi On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Rouhi I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem. cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: Dear Bruce I am working on Freesurfer 2 caret meshes. I am using FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created? Thank you very much Rouhi On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Try using fsaverage as the trgsubject Cheers Bruce On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage 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. -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi-- With Best Regards Rouhollah Abdollahi
where can I upload one subject? which I have problem with that subject in RH registraton.
On Sat, Aug 13, 2011 at 10:30 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
if the aseg is good I don't see how it's possible that we don't know about the 90 deg rotation. If you upload the dataset I'll take a look On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote:
Hi BruceI think the aseg is good but only rotated 90 degree. I will try
to rotate sphere to see how it will create sphere.reg.
On Sat, Aug 13, 2011 at 1:02 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Matt
if they were tipped forward 90deg and we didn't detect it I wouldthink that the aseg would fail catastrophically. Did that happen? Bruce
On Fri, 12 Aug 2011, Matt Glasser wrote:
So I thought the issue had been solved, but perhaps not. Bruce, we(i.e. David) think the problem with Rouhi?s data is that FreeSurfer did not detect that the original images were tipped forward 90 degrees and as a result the surface registration failed intermittently (i.e. in some subjects it okay, but in others it is not). These data were created with a fairly old version of FreeSurfer (Rouhi can give the version number), and then a significant amount of manual effort was put into defining some retinotopy on the data. Therefore it isn?t really a feasible option to just rerun the data with a newer version of FreeSurfer, but we want to make use of accurate FreeSurfer surface registration to make group average retinotopy results. So the question is how do we go about making sure the spheres are initialized to have the correct rigid orientation before the registration proceeds.
Thanks, Matt. ______________________________**______________________________**______________________________**______________________________** _________________________
From: freesurfer-bounces@nmr.mgh.**harvard.edu<freesurfer-bounces@nmr.mgh.harvard.edu>[mailto:freesurfer-bounces@**nmr.mgh.harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi Sent: Friday, August 12, 2011 12:38 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Label2label on fsaverage
I tried to rotate the surface by tksurfer and save it as new file .But when I open the new surface like white it was not rotated. Is there any special thing that I have to do?
Best Rouhi On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote:
Dear Bruce If I want to rotate sucli pattern too if it is the same? On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
I guess you could rotate the surfaces, save them, then resample thelabels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this.
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think the easiest way is to create all surfaces again but withcorrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?!
Bests Rouhi On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files. On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: not easily. Why would you need to do such a thing? On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set? Best Rouhi On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Rouhi I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem. cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: Dear Bruce I am working on Freesurfer 2 caret meshes. I am using **FreeSurfer2CaretConvertAndRegi**sterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created? Thank you very much Rouhi On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Try using fsaverage as the trgsubject Cheers Bruce On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --**0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage 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. -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi-- With Best Regards Rouhollah Abdollahi
you can either ftp it or put it on our file drop (you can find both on our wiki) On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote:
where can I upload one subject? which I have problem with that subject in RH registraton.
On Sat, Aug 13, 2011 at 10:30 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: if the aseg is good I don't see how it's possible that we don't know about the 90 deg rotation. If you upload the dataset I'll take a look On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote:
Hi BruceI think the aseg is good but only rotated 90 degree. I will try to rotate sphere to see how it will create sphere.reg.On Sat, Aug 13, 2011 at 1:02 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Matt
if they were tipped forward 90deg and we didn't detect it I would think that the aseg would fail catastrophically. Did that happen? Bruce
On Fri, 12 Aug 2011, Matt Glasser wrote:
So I thought the issue had been solved, but perhaps not. Bruce, we (i.e. David) think the problem with Rouhi?s data is that FreeSurfer did not detect that the original images were tipped forward 90 degrees and as a result the surface registration failed intermittently (i.e. in some subjects it okay, but in others it is not). These data were created with a fairly old version of FreeSurfer (Rouhi can give the version number), and then a significant amount of manual effort was put into defining some retinotopy on the data. Therefore it isn?t really a feasible option to just rerun the data with a newer version of FreeSurfer, but we want to make use of accurate FreeSurfer surface registration to make group average retinotopy results. So the question is how do we go about making sure the spheres are initialized to have the correct rigid orientation before the registration proceeds.
Thanks,
Matt.
_________________________________________________________________________________________________________________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi Sent: Friday, August 12, 2011 12:38 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Label2label on fsaverage
I tried to rotate the surface by tksurfer and save it as new file . But when I open the new surface like white it was not rotated. Is there any special thing that I have to do?
Best Rouhi
On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi roohy466@gmail.com wrote:
Dear Bruce If I want to rotate sucli pattern too if it is the same?
On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I guess you could rotate the surfaces, save them, then resample the labels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this.
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce I think the easiest way is to create all surfaces again but with corrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?!
Bests Rouhi
On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files.
On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: not easily. Why would you need to do such a thing?
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce
I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set?
Best Rouhi
On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Rouhi
I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem.
cheers Bruce
On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem.
Thanks for your quick response.
On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi roohy466@gmail.com wrote: Dear Bruce
I am working on Freesurfer 2 caret meshes. I am using FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created?
Thank you very much
Rouhi
On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Try using fsaverage as the trgsubject Cheers Bruce
On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi roohy466@gmail.com wrote:
> .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage
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.
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
--
With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
Hi Bruce, My problem has been solved. I rotate the ?h.sphere by mris_rotate <source> 0 0 90 <output> and then I used mris_register to register it to fsaverage and I saw my result is perfectly registered to fsaverage. it means that mris_register was not able to realign the sphere to fsaverage if the original orientation is bigger than some degrees like 90. I don't think you need to spend time on it. thanks alot for your helps.
bests Rouhi
On Sat, Aug 13, 2011 at 11:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
you can either ftp it or put it on our file drop (you can find both on our wiki)
On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote:
where can I upload one subject? which I have problem with that subject in
RH registraton.
On Sat, Aug 13, 2011 at 10:30 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: if the aseg is good I don't see how it's possible that we don't know about the 90 deg rotation. If you upload the dataset I'll take a look On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote:
Hi BruceI think the aseg is good but only rotated 90 degree. Iwill try to rotate sphere to see how it will create sphere.reg.
On Sat, Aug 13, 2011 at 1:02 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Matt
if they were tipped forward 90deg and we didn't detect it I wouldthink that the aseg would fail catastrophically. Did that happen? Bruce
On Fri, 12 Aug 2011, Matt Glasser wrote:
So I thought the issue had been solved, but perhaps not. Bruce, we(i.e. David) think the problem with Rouhi?s data is that FreeSurfer did not detect that the original images were tipped forward 90 degrees and as a result the surface registration failed intermittently (i.e. in some subjects it okay, but in others it is not). These data were created with a fairly old version of FreeSurfer (Rouhi can give the version number), and then a significant amount of manual effort was put into defining some retinotopy on the data. Therefore it isn?t really a feasible option to just rerun the data with a newer version of FreeSurfer, but we want to make use of accurate FreeSurfer surface registration to make group average retinotopy results. So the question is how do we go about making sure the spheres are initialized to have the correct rigid orientation before the registration proceeds.
Thanks, Matt._____________________________**______________________________** ______________________________**______________________________** __________________________
From: freesurfer-bounces@nmr.mgh.**harvard.edu<freesurfer-bounces@nmr.mgh.harvard.edu>[mailto:freesurfer-bounces@**nmr.mgh.harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi Sent: Friday, August 12, 2011 12:38 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Label2label on fsaverage
I tried to rotate the surface by tksurfer and save it as new file .But when I open the new surface like white it was not rotated. Is there any special thing that I have to do?
Best Rouhi On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote:
Dear Bruce If I want to rotate sucli pattern too if it is the same? On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
I guess you could rotate the surfaces, save them, then resample thelabels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this.
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think the easiest way is to create all surfaces again but withcorrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?!
Bests Rouhi On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files. On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: not easily. Why would you need to do such a thing? On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set? Best Rouhi On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Rouhi I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem. cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: Dear Bruce I am working on Freesurfer 2 caret meshes. I am using **FreeSurfer2CaretConvertAndRegi**sterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created? Thank you very much Rouhi On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Try using fsaverage as the trgsubject Cheers Bruce On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --**0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage 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. -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
ok. I have to admit to being puzzled as to how everything else in recon-all worked with a rotation that big
Bruce
On Sun, 14 Aug 2011, Rouhollah Abdollahi wrote:
Hi Bruce,My problem has been solved. I rotate the ?h.sphere by mris_rotate <source> 0 0 90 <output> and then I used mris_register to register it to fsaverage and I saw my result is perfectly registered to fsaverage. it means that mris_register was not able to realign the sphere to fsaverage if the original orientation is bigger than some degrees like 90. I don't think you need to spend time on it. thanks alot for your helps.
bests Rouhi
On Sat, Aug 13, 2011 at 11:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: you can either ftp it or put it on our file drop (you can find both on our wiki)
On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote:
where can I upload one subject? which I have problem with that subject in RH registraton. On Sat, Aug 13, 2011 at 10:30 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: if the aseg is good I don't see how it's possible that we don't know about the 90 deg rotation. If you upload the dataset I'll take a look On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote: Hi BruceI think the aseg is good but only rotated 90 degree. I will try to rotate sphere to see how it will create sphere.reg. On Sat, Aug 13, 2011 at 1:02 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Matt if they were tipped forward 90deg and we didn't detect it I would think that the aseg would fail catastrophically. Did that happen? Bruce On Fri, 12 Aug 2011, Matt Glasser wrote: So I thought the issue had been solved, but perhaps not. Bruce, we (i.e. David) think the problem with Rouhi?s data is that FreeSurfer did not detect that the original images were tipped forward 90 degrees and as a result the surface registration failed intermittently (i.e. in some subjects it okay, but in others it is not). These data were created with a fairly old version of FreeSurfer (Rouhi can give the version number), and then a significant amount of manual effort was put into defining some retinotopy on the data. Therefore it isn?t really a feasible option to just rerun the data with a newer version of FreeSurfer, but we want to make use of accurate FreeSurfer surface registration to make group average retinotopy results. So the question is how do we go about making sure the spheres are initialized to have the correct rigid orientation before the registration proceeds. Thanks, Matt. _________________________________________________________________________________________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi Sent: Friday, August 12, 2011 12:38 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Label2label on fsaverage I tried to rotate the surface by tksurfer and save it as new file . But when I open the new surface like white it was not rotated. Is there any special thing that I have to do? Best Rouhi On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: Dear Bruce If I want to rotate sucli pattern too if it is the same? On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: I guess you could rotate the surfaces, save them, then resample the labels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this. On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think the easiest way is to create all surfaces again but with corrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?! Bests Rouhi On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files. On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: not easily. Why would you need to do such a thing? On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set? Best Rouhi On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Rouhi I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem. cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: Dear Bruce I am working on Freesurfer 2 caret meshes. I am using FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created? Thank you very much Rouhi On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Try using fsaverage as the trgsubject Cheers Bruce On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage 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. -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi-- With Best Regards Rouhollah Abdollahi
oh, that won't work. That's just for visualization, it doesn't actually change any coordinates. As I said, we don't usually do this. If you can come up with a rotation matrix I guess either mri_surf2surf or mris_transform would work
cheers Bruce On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
I tried to rotate the surface by tksurfer and save it as new file . But when I open the new surface like white it was not rotated. Is there any special thing that I have to do?
Best Rouhi
On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi roohy466@gmail.com wrote: Dear Bruce If I want to rotate sucli pattern too if it is the same?
On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: I guess you could rotate the surfaces, save them, then resample the labels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this.
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce I think the easiest way is to create all surfaces again but with corrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?! Bests Rouhi On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files. On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: not easily. Why would you need to do such a thing? On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set? Best Rouhi On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Rouhi I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem. cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: Dear Bruce I am working on Freesurfer 2 caret meshes. I am using FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created? Thank you very much Rouhi On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Try using fsaverage as the trgsubject Cheers Bruce On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage 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. -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi
you won't need to rotate them. They are attached to the surface, so if the surface is rotated, they will be too On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce If I want to rotate sucli pattern too if it is the same?
On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: I guess you could rotate the surfaces, save them, then resample the labels so that they get the new surface coords and sample them into the volume, then onto the newly created surfaces. Not sure, we haven't ever had to do anything like this.
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce I think the easiest way is to create all surfaces again but with corrected and well aligned brain. The next step for me to create new labels from old labels based on white surface (90 degree rotated) to new white surface. But how? Is there any way to do that? I mean like label2label or surf2surf if two surfaces are the same but one of them only rotated?! Bests Rouhi On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: I don't see how anything would work if it was off by 90deg, but I guess you should try it On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Because I am using a result from a very old experiment that done on wrong direction and the orig.mgz s are not oriented according to freesurfer template. I cannot creat white because all results that I have (label files) are on white surface. The only way that I think I need to realign all surfaces and volume and apply that rotation on my label files. On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: not easily. Why would you need to do such a thing? On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set? Best Rouhi On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Rouhi I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem. cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: Dear Bruce I am working on Freesurfer 2 caret meshes. I am using FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created? Thank you very much Rouhi On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Try using fsaverage as the trgsubject Cheers Bruce On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466@gmail.com> wrote: > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > I've tried to export my label file from individual space to fsaverage space by using this command: > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > like it is not deformed properly. > Is it related to registration to fsaverage or something esle? > The question is how I can register the subjects surfaces to fsaverage 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. -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi -- With Best Regards Rouhollah Abdollahi-- With Best Regards Rouhollah Abdollahi
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Matt Glasser -
Rouhollah Abdollahi