Hi Sandra, (and the list, I think this might be interesting for others)
1. the longitudinal ?h.thickness files are in registration (within subject) so in order to compute the difference or the rate you can simply use: mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness and for the rate, you can divide by time 1 thickness or by the average thickness. If the time points are not equally spaced across subjects, you can also divide by difference in time. It is best to smooth the thickness files before you do all this (i.e. within time point smooth the ?h.thickness files with mri_surf2surf).
2. then map everything to your template (e.g. fsaverage) with mri_surf2surf
3. there you can stack the thick-differences or thick-rates with mri_concat
4. do the glm
Beste Gruesse, Martin
On Tue, 2010-06-29 at 21:50 +0200, Sandra Duezel wrote:
Hi Martin
I just have got your answer to the longitudinal processing question from Michele and have some other questions regarding the output data from the longitudinal stream. Our study contains MRI scans of 45 elderly subjects from 2 timepoints. I have done all steps from the longitudinal stream and it worked without any problems.
Now I would like calculate the thickness difference maps between the prae and post scans, which are already longitudinally processed.
I have tried the thickdiffmap-script using the <tp1>.long and <tp2>.long data. It creates a .mgz file in each subject but also a new folder "groupstudy" with the prae/post data resampled to fsaverage (its an .mgh file)
Is this the right way to calculate the difference for longitudinal data?
Do I also need to proceed with GLM analysis as suggestet in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do I need to handle the longitudial data in a different way?
Thank you very much for your help and answers!
Best regards
Sandra
Am 29.06.2010 um 17:24 schrieb Martin Reuter:
There is a step by step description on the longitudinal stream. It basically means:
- to process your two time points individually through freesurfer
(standard processing). 2. to create a template for each subjects from these processed time points 3. to run the two time points again (passing it the template) to compute better longitudinal results (less variability, more accuracy).
Alternatively, you can run mris_preproc for both time point 1 and 2 to create separate files with all your subjects in them, then use mris_calc like below to create a difference file, then follow the standard command-line stream as is described on the wiki.
doug
Martin Reuter wrote:
Hi Sandra, (and the list, I think this might be interesting for others)
the longitudinal ?h.thickness files are in registration (within subject) so in order to compute the difference or the rate you can simply use: mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness and for the rate, you can divide by time 1 thickness or by the average thickness. If the time points are not equally spaced across subjects, you can also divide by difference in time. It is best to smooth the thickness files before you do all this (i.e. within time point smooth the ?h.thickness files with mri_surf2surf).
then map everything to your template (e.g. fsaverage) with mri_surf2surf
- there you can stack the thick-differences or thick-rates with
mri_concat
- do the glm
Beste Gruesse, Martin
On Tue, 2010-06-29 at 21:50 +0200, Sandra Duezel wrote:
Hi Martin
I just have got your answer to the longitudinal processing question from Michele and have some other questions regarding the output data from the longitudinal stream. Our study contains MRI scans of 45 elderly subjects from 2 timepoints. I have done all steps from the longitudinal stream and it worked without any problems.
Now I would like calculate the thickness difference maps between the prae and post scans, which are already longitudinally processed.
I have tried the thickdiffmap-script using the <tp1>.long and <tp2>.long data. It creates a .mgz file in each subject but also a new folder "groupstudy" with the prae/post data resampled to fsaverage (its an .mgh file)
Is this the right way to calculate the difference for longitudinal data?
Do I also need to proceed with GLM analysis as suggestet in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do I need to handle the longitudial data in a different way?
Thank you very much for your help and answers!
Best regards
Sandra
Am 29.06.2010 um 17:24 schrieb Martin Reuter:
There is a step by step description on the longitudinal stream. It basically means:
- to process your two time points individually through freesurfer
(standard processing). 2. to create a template for each subjects from these processed time points 3. to run the two time points again (passing it the template) to compute better longitudinal results (less variability, more accuracy).
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Martin and Douglas,
I had the same question as Sandra and searching the mailing list I found your answers. However, it is not still clear for me which data I need to use for the mris_calc (reply from Martin) or mris_preproc (reply from Douglas), i.e. (<tp1> & <tp2>) or (<tp1>.long.<template_id> & <tp2>.long.<template_id>). Could you please clarify it for me?
Thanks in advance,
Sima.
On Tue, Jun 29, 2010 at 9:34 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Alternatively, you can run mris_preproc for both time point 1 and 2 to create separate files with all your subjects in them, then use mris_calc like below to create a difference file, then follow the standard command-line stream as is described on the wiki.
doug
Martin Reuter wrote:
Hi Sandra, (and the list, I think this might be interesting for others)
the longitudinal ?h.thickness files are in registration (within subject) so in order to compute the difference or the rate you can simply use: mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness and for the rate, you can divide by time 1 thickness or by the average thickness. If the time points are not equally spaced across subjects, you can also divide by difference in time. It is best to smooth the thickness files before you do all this (i.e. within time point smooth the ?h.thickness files with mri_surf2surf).
then map everything to your template (e.g. fsaverage) with mri_surf2surf
- there you can stack the thick-differences or thick-rates with
mri_concat
- do the glm
Beste Gruesse, Martin
On Tue, 2010-06-29 at 21:50 +0200, Sandra Duezel wrote:
Hi Martin
I just have got your answer to the longitudinal processing question from Michele and have some other questions regarding the output data from the longitudinal stream. Our study contains MRI scans of 45 elderly subjects from 2 timepoints. I have done all steps from the longitudinal stream and it worked without any problems.
Now I would like calculate the thickness difference maps between the prae and post scans, which are already longitudinally processed.
I have tried the thickdiffmap-script using the <tp1>.long and <tp2>.long data. It creates a .mgz file in each subject but also a new folder "groupstudy" with the prae/post data resampled to fsaverage (its an .mgh file)
Is this the right way to calculate the difference for longitudinal data?
Do I also need to proceed with GLM analysis as suggestet in
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
or do I need to handle the longitudial data in a different way?
Thank you very much for your help and answers!
Best regards
Sandra
Am 29.06.2010 um 17:24 schrieb Martin Reuter:
There is a step by step description on the longitudinal stream. It basically means:
- to process your two time points individually through freesurfer
(standard processing). 2. to create a template for each subjects from these processed time points 3. to run the two time points again (passing it the template) to compute better longitudinal results (less variability, more accuracy).
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Hi always use the data from tp.long.base , they are less variable and more accurate than the cross sectional results. (that is why you tun the long stream at all).
Best Martin
On 27.10.2010, at 09:13, sima chalavi sima.chalavi@gmail.com wrote:
Dear Martin and Douglas, I had the same question as Sandra and searching the mailing list I found your answers. However, it is not still clear for me which data I need to use for the mris_calc (reply from Martin) or mris_preproc (reply from Douglas), i.e. (<tp1> & <tp2>) or (<tp1>.long.<template_id> & <tp2>.long.<template_id>). Could you please clarify it for me? Thanks in advance, Sima.
On Tue, Jun 29, 2010 at 9:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: Alternatively, you can run mris_preproc for both time point 1 and 2 to create separate files with all your subjects in them, then use mris_calc like below to create a difference file, then follow the standard command-line stream as is described on the wiki.
doug
Martin Reuter wrote:
Hi Sandra, (and the list, I think this might be interesting for others)
the longitudinal ?h.thickness files are in registration (within subject) so in order to compute the difference or the rate you can simply use: mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness and for the rate, you can divide by time 1 thickness or by the average thickness. If the time points are not equally spaced across subjects, you can also divide by difference in time. It is best to smooth the thickness files before you do all this (i.e. within time point smooth the ?h.thickness files with mri_surf2surf).
then map everything to your template (e.g. fsaverage) with mri_surf2surf
- there you can stack the thick-differences or thick-rates with
mri_concat
- do the glm
Beste Gruesse, Martin
On Tue, 2010-06-29 at 21:50 +0200, Sandra Duezel wrote:
Hi Martin
I just have got your answer to the longitudinal processing question from Michele and have some other questions regarding the output data from the longitudinal stream. Our study contains MRI scans of 45 elderly subjects from 2 timepoints. I have done all steps from the longitudinal stream and it worked without any problems.
Now I would like calculate the thickness difference maps between the prae and post scans, which are already longitudinally processed.
I have tried the thickdiffmap-script using the <tp1>.long and <tp2>.long data. It creates a .mgz file in each subject but also a new folder "groupstudy" with the prae/post data resampled to fsaverage (its an .mgh file)
Is this the right way to calculate the difference for longitudinal data?
Do I also need to proceed with GLM analysis as suggestet in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do I need to handle the longitudial data in a different way?
Thank you very much for your help and answers!
Best regards
Sandra
Am 29.06.2010 um 17:24 schrieb Martin Reuter:
There is a step by step description on the longitudinal stream. It basically means:
- to process your two time points individually through freesurfer
(standard processing). 2. to create a template for each subjects from these processed time points 3. to run the two time points again (passing it the template) to compute better longitudinal results (less variability, more accuracy).
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Martin Reuter -
Martin Reutet
-
sima chalavi