Hi,
I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 computer using freesurfer 4.5. I have SPM 8 and FSL also installed.
I have two versions of matlab (matlab R2009b & R2008a) on my computer. I think spm runs through the R2009b on my computer. I have added the SPM path to the startup.m of both matlabs by adding the following line (they both point to the same startup.m ):
path(path,'/Applications/spm8');
I run preprocessing on the data using the following command:
preproc-sess -nosmooth -sf retino-sess -df retino.dir
then I run automatic registration with the following command:
spmregister-sess -sf retino-sess -df retino.dir
It runs smoothly and there seems to be no errors. But when I try to check the registration with this command:
tkregister-sess -sf retino-sess -df retino.dir -inorm
what I see is not a good registration. Isn't spm register supposed to do a good job in automatic registration? The one that I get still needs a lot of manual adjustment. Am I doing something wrong? I have attached the log files for spmregister and tkregister and a screen shot of the image that I get after running tkregister. I would appreciate any help in this matter.
Thanks,
Maryam
Hi Maryam,
You should check your spm defaults to see whether it uses radiology or neurology convention. Most likely your spm has flipped your image, and the spmregister-sess is trying to match the left hemisphere of your functionals to the right hemisphere of your anatomical.
-Yuhong
On Thu, Feb 3, 2011 at 9:59 PM, Maryam Vaziri Pashkam mvaziri.p@gmail.comwrote:
Hi,
I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 computer using freesurfer 4.5. I have SPM 8 and FSL also installed.
I have two versions of matlab (matlab R2009b & R2008a) on my computer. I think spm runs through the R2009b on my computer. I have added the SPM path to the startup.m of both matlabs by adding the following line (they both point to the same startup.m ):
path(path,'/Applications/spm8');
I run preprocessing on the data using the following command:
preproc-sess -nosmooth -sf retino-sess -df retino.dir
then I run automatic registration with the following command:
spmregister-sess -sf retino-sess -df retino.dir
It runs smoothly and there seems to be no errors. But when I try to check the registration with this command:
tkregister-sess -sf retino-sess -df retino.dir -inorm
what I see is not a good registration. Isn't spm register supposed to do a good job in automatic registration? The one that I get still needs a lot of manual adjustment. Am I doing something wrong? I have attached the log files for spmregister and tkregister and a screen shot of the image that I get after running tkregister. I would appreciate any help in this matter.
Thanks,
Maryam
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.
Can you tell me how to check that because I"m having the same problem with spmregister-sess with my linux as well and I've never used SPM at all, and honestly can't even figure out how to open it.
Katie
On Thu, Feb 3, 2011 at 11:21 PM, Y.V. Jiang yuhong.jiang@gmail.com wrote:
Hi Maryam,
You should check your spm defaults to see whether it uses radiology or neurology convention. Most likely your spm has flipped your image, and the spmregister-sess is trying to match the left hemisphere of your functionals to the right hemisphere of your anatomical.
-Yuhong
On Thu, Feb 3, 2011 at 9:59 PM, Maryam Vaziri Pashkam <mvaziri.p@gmail.com
wrote:
Hi,
I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 computer using freesurfer 4.5. I have SPM 8 and FSL also installed.
I have two versions of matlab (matlab R2009b & R2008a) on my computer. I think spm runs through the R2009b on my computer. I have added the SPM path to the startup.m of both matlabs by adding the following line (they both point to the same startup.m ):
path(path,'/Applications/spm8');
I run preprocessing on the data using the following command:
preproc-sess -nosmooth -sf retino-sess -df retino.dir
then I run automatic registration with the following command:
spmregister-sess -sf retino-sess -df retino.dir
It runs smoothly and there seems to be no errors. But when I try to check the registration with this command:
tkregister-sess -sf retino-sess -df retino.dir -inorm
what I see is not a good registration. Isn't spm register supposed to do a good job in automatic registration? The one that I get still needs a lot of manual adjustment. Am I doing something wrong? I have attached the log files for spmregister and tkregister and a screen shot of the image that I get after running tkregister. I would appreciate any help in this matter.
Thanks,
Maryam
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.
--
Yuhong Vanessa Jiang, PhD, Associate Professor & McKnight Presidential Fellow Department of Psychology, Univ of Minnesota jiang166@umn.edu, 612-625-7003 https://sites.google.com/site/jiang166/
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.
It depends on which version of SPM you're running. It's either the file called spm_defaults.m, or on my system it's file called spm_flip_analyze_images.m. There is a line that says:
flip = 1; (or flip = 0). For my kind of scans I need to set flip = 0, whereas the spm defaults tend to come with flip = 1 (which turns your radiology images into neurology images).
-Yuhong
On Fri, Feb 4, 2011 at 10:30 AM, Katie Bettencourt kcb@wjh.harvard.eduwrote:
Can you tell me how to check that because I"m having the same problem with spmregister-sess with my linux as well and I've never used SPM at all, and honestly can't even figure out how to open it.
Katie
On Thu, Feb 3, 2011 at 11:21 PM, Y.V. Jiang yuhong.jiang@gmail.comwrote:
Hi Maryam,
You should check your spm defaults to see whether it uses radiology or neurology convention. Most likely your spm has flipped your image, and the spmregister-sess is trying to match the left hemisphere of your functionals to the right hemisphere of your anatomical.
-Yuhong
On Thu, Feb 3, 2011 at 9:59 PM, Maryam Vaziri Pashkam < mvaziri.p@gmail.com> wrote:
Hi,
I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 computer using freesurfer 4.5. I have SPM 8 and FSL also installed.
I have two versions of matlab (matlab R2009b & R2008a) on my computer. I think spm runs through the R2009b on my computer. I have added the SPM path to the startup.m of both matlabs by adding the following line (they both point to the same startup.m ):
path(path,'/Applications/spm8');
I run preprocessing on the data using the following command:
preproc-sess -nosmooth -sf retino-sess -df retino.dir
then I run automatic registration with the following command:
spmregister-sess -sf retino-sess -df retino.dir
It runs smoothly and there seems to be no errors. But when I try to check the registration with this command:
tkregister-sess -sf retino-sess -df retino.dir -inorm
what I see is not a good registration. Isn't spm register supposed to do a good job in automatic registration? The one that I get still needs a lot of manual adjustment. Am I doing something wrong? I have attached the log files for spmregister and tkregister and a screen shot of the image that I get after running tkregister. I would appreciate any help in this matter.
Thanks,
Maryam
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.
--
Yuhong Vanessa Jiang, PhD, Associate Professor & McKnight Presidential Fellow Department of Psychology, Univ of Minnesota jiang166@umn.edu, 612-625-7003 https://sites.google.com/site/jiang166/
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.
The spm_flip_analyse_images.m was what I needed! Thanks so much!
Katie
On Fri, Feb 4, 2011 at 11:53 AM, Y.V. Jiang yuhong.jiang@gmail.com wrote:
It depends on which version of SPM you're running. It's either the file called spm_defaults.m, or on my system it's file called spm_flip_analyze_images.m. There is a line that says:
flip = 1; (or flip = 0). For my kind of scans I need to set flip = 0, whereas the spm defaults tend to come with flip = 1 (which turns your radiology images into neurology images).
-Yuhong
On Fri, Feb 4, 2011 at 10:30 AM, Katie Bettencourt kcb@wjh.harvard.eduwrote:
Can you tell me how to check that because I"m having the same problem with spmregister-sess with my linux as well and I've never used SPM at all, and honestly can't even figure out how to open it.
Katie
On Thu, Feb 3, 2011 at 11:21 PM, Y.V. Jiang yuhong.jiang@gmail.comwrote:
Hi Maryam,
You should check your spm defaults to see whether it uses radiology or neurology convention. Most likely your spm has flipped your image, and the spmregister-sess is trying to match the left hemisphere of your functionals to the right hemisphere of your anatomical.
-Yuhong
On Thu, Feb 3, 2011 at 9:59 PM, Maryam Vaziri Pashkam < mvaziri.p@gmail.com> wrote:
Hi,
I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 computer using freesurfer 4.5. I have SPM 8 and FSL also installed.
I have two versions of matlab (matlab R2009b & R2008a) on my computer. I think spm runs through the R2009b on my computer. I have added the SPM path to the startup.m of both matlabs by adding the following line (they both point to the same startup.m ):
path(path,'/Applications/spm8');
I run preprocessing on the data using the following command:
preproc-sess -nosmooth -sf retino-sess -df retino.dir
then I run automatic registration with the following command:
spmregister-sess -sf retino-sess -df retino.dir
It runs smoothly and there seems to be no errors. But when I try to check the registration with this command:
tkregister-sess -sf retino-sess -df retino.dir -inorm
what I see is not a good registration. Isn't spm register supposed to do a good job in automatic registration? The one that I get still needs a lot of manual adjustment. Am I doing something wrong? I have attached the log files for spmregister and tkregister and a screen shot of the image that I get after running tkregister. I would appreciate any help in this matter.
Thanks,
Maryam
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.
--
Yuhong Vanessa Jiang, PhD, Associate Professor & McKnight Presidential Fellow Department of Psychology, Univ of Minnesota jiang166@umn.edu, 612-625-7003 https://sites.google.com/site/jiang166/
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.
--
Yuhong Vanessa Jiang, PhD, Associate Professor & McKnight Presidential Fellow Department of Psychology, Univ of Minnesota jiang166@umn.edu, 612-625-7003 https://sites.google.com/site/jiang166/
freesurfer@nmr.mgh.harvard.edu
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Katie Bettencourt -
Maryam Vaziri Pashkam -
Y.V. Jiang