Hi all I want to use a freesurfer parcellation as a seed point in DTI analysis using a non-FSL DTI tractography tool. I have the raw DTI images for around 40 subjects (20 scz 20 controls). From the structural MPRAGEs that correspond to these subjects, I have an average image where I have my defined ROI (which is a freesurfer atlas based parcellation). The ROI has numerous vertices whose MNI coordinates are available to me. Please correct me if I have understood this properly 1. I have to process the raw DTI images to obtain FA/trace images first for each subject 2. each FA/trace image should be registered to the average structural MPRAGE of the group How do I then go on to obtain the coordinates for my label on the DTI space?
Many thanks Lena
_______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
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I'm not sure what it is that you need. Do you need seed coordinates in the native DTI space of each subject or in MNI space? If MNI, which one, mni152 or mni305? Do you need the coordinates in xyz or row,col,slice? Or do you need your seed region to be a mask (in what space)?
doug
On 8/12/10 8:55 AM, Lena Palaniyappan wrote:
Hi all I want to use a freesurfer parcellation as a seed point in DTI analysis using a non-FSL DTI tractography tool. I have the raw DTI images for around 40 subjects (20 scz 20 controls). From the structural MPRAGEs that correspond to these subjects, I have an average image where I have my defined ROI (which is a freesurfer atlas based parcellation). The ROI has numerous vertices whose MNI coordinates are available to me. Please correct me if I have understood this properly
- I have to process the raw DTI images to obtain FA/trace images first for each subject
- each FA/trace image should be registered to the average structural MPRAGE of the group
How do I then go on to obtain the coordinates for my label on the DTI space?
Many thanks Lena
*Lena Palaniyappan *Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Doug I need an analyze file with the two regions I am interested in each individuals DTI space The rois are anterior insula and posterior insula from Destrieux atlas 2009 Cheers Lena
On 12/08/2010 15:07, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
I'm not sure what it is that you need. Do you need seed coordinates in the native DTI space of each subject or in MNI space? If MNI, which one, mni152 or mni305? Do you need the coordinates in xyz or row,col,slice? Or do you need your seed region to be a mask (in what space)?
doug
On 8/12/10 8:55 AM, Lena Palaniyappan wrote:
Coordinates for DTI tractography Hi all I want to use a freesurfer parcellation as a seed point in DTI analysis using a non-FSL DTI tractography tool. I have the raw DTI images for around 40 subjects (20 scz 20 controls). From the structural MPRAGEs that correspond to these subjects, I have an average image where I have my defined ROI (which is a freesurfer atlas based parcellation). The ROI has numerous vertices whose MNI coordinates are available to me. Please correct me if I have understood this properly
- I have to process the raw DTI images to obtain FA/trace images first for
each subject 2. each FA/trace image should be registered to the average structural MPRAGE of the group 3. How do I then go on to obtain the coordinates for my label on the DTI space?
Many thanks Lena
Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
Then use bbregister on the native-space low-b image to create a register.dat. Then use mri_label2vol to map the aparc+aseg.mgz to the native DTI space. Then use mri_binarize to create binary masks for each of your ROIs.
doug
On 8/12/10 10:52 AM, Lena Palaniyappan wrote:
Doug I need an analyze file with the two regions I am interested in each individuals DTI space The rois are anterior insula and posterior insula from Destrieux atlas 2009 Cheers Lena
On 12/08/2010 15:07, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
I'm not sure what it is that you need. Do you need seed coordinates in the native DTI space of each subject or in MNI space? If MNI, which one, mni152 or mni305? Do you need the coordinates in xyz or row,col,slice? Or do you need your seed region to be a mask (in what space)? doug On 8/12/10 8:55 AM, Lena Palaniyappan wrote: Coordinates for DTI tractography Hi all I want to use a freesurfer parcellation as a seed point in DTI analysis using a non-FSL DTI tractography tool. I have the raw DTI images for around 40 subjects (20 scz 20 controls). From the structural MPRAGEs that correspond to these subjects, I have an average image where I have my defined ROI (which is a freesurfer atlas based parcellation). The ROI has numerous vertices whose MNI coordinates are available to me. Please correct me if I have understood this properly 1. I have to process the raw DTI images to obtain FA/trace images first for each subject 2. each FA/trace image should be registered to the average structural MPRAGE of the group 3. How do I then go on to obtain the coordinates for my label on the DTI space? Many thanks Lena _______________________________________________________ *Lena Palaniyappan *Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
*Lena Palaniyappan *Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Lena Palaniyappan