Dear Doug,
Thanks a lot for your advice.
We followed the examples on the wiki (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#AssembletheDa...) and tried to analyze our data as described. We have a single group with two continuous covariates. Therefore we created the freesurfer descriptor file (g1v2_I.fsgd) and three contrast files (main.mtx; age.mtx; Amputationsdauer.mtx). The preprocessing finished without error for both hemispheres.
The following command line we used for the preprocessing: mris_preproc --fsgd qdec/GLM/g1v2_I.fsgd --cache-in long.thickness-avg.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.g1v2_I.thickness.10.mgh
After this we tried the mri_glmfit for our longitudinal data. Our command line was the following: mri_glmfit --glmdir g1v2_I --y lh.g1v2_I.thickness.10.mgh --fsgd qdec/GLM/g1v2_I.fsgd --C qdec/GLM/main.mtx --C qdec/GLM/age.mtx --C qdec/GLM/Amputationsdauer.mtx
We get the error message: ERROR: you must use '--surface subject hemi' with surface data
Therfore we tried to specify
subject as fsaverage, hemi as lh, surface as thickness.
Unfortunately, this did not work out and other alternative approaches to solve this problem did not function as well.
Do we have to create a subject descriptor file for our longitudinal templates? Or did we miss anything else? We thought about creating the --X design matrix file for longitudinal data, we found the instruction for between factors. But this could not work for our data.
Best regards Sandra
-----Nachricht von greve@nmr.mgh.harvard.edu -----Datum: Fri, 28 Jun 2013 10:40:57 -0400 Von: Douglas N Greve greve@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] longitudinal analyses for one group An: freesurfer@nmr.mgh.harvard.edu
Hi Sandra, you cannot do the longitudinal statistical analysis in QDEC. You will have to use mri_glmfit. Look at the FSGD examples on the wiki. doug
On 06/28/2013 03:28 AM, Sandra Preissler wrote:
[Zitattext verstecken] Dear freesurfer experts,
we want to do longitudinal analyses for two different time points in only one group (We do not have a control group or different groups within the intervention). So we did the longitudinal processing as described in the tutorial
(http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#Prepar...). Now we tried to investigate the results with Qdec. We wanted to test whether the averaged change of thickness between pre-test and post-test differs from zero. We had the experience that we could only test the averaged thickness by choosing a discrete factor in Qdec. Our Problem is that we don't have a control group. So we couldn't choose the group variable as discrete factor. It's an pre-post-design with only one group.
Is it possible to investigate changes in thickness between pre-test and post-test without choosing a factor? Or do we have to create a group variable as discrete factor?
Can you help us in fixing this problem?
Thanks in advance!
Sandra
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Sandra, what was your final command line? doug
On 07/03/2013 06:28 AM, Sandra Preissler wrote:
Dear Doug,
Thanks a lot for your advice.
We followed the examples on the wiki (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#AssembletheDa...) and tried to analyze our data as described. We have a single group with two continuous covariates. Therefore we created the freesurfer descriptor file (g1v2_I.fsgd) and three contrast files (main.mtx; age.mtx; Amputationsdauer.mtx). The preprocessing finished without error for both hemispheres.
The following command line we used for the preprocessing: mris_preproc --fsgd qdec/GLM/g1v2_I.fsgd --cache-in long.thickness-avg.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.g1v2_I.thickness.10.mgh
After this we tried the mri_glmfit for our longitudinal data. Our command line was the following: mri_glmfit --glmdir g1v2_I --y lh.g1v2_I.thickness.10.mgh --fsgd qdec/GLM/g1v2_I.fsgd --C qdec/GLM/main.mtx --C qdec/GLM/age.mtx --C qdec/GLM/Amputationsdauer.mtx
We get the error message: ERROR: you must use '--surface subject hemi' with surface data
Therfore we tried to specify
subject as fsaverage, hemi as lh, surface as thickness.
Unfortunately, this did not work out and other alternative approaches to solve this problem did not function as well.
Do we have to create a subject descriptor file for our longitudinal templates? Or did we miss anything else? We thought about creating the --X “design matrix file” for longitudinal data, we found the instruction for between factors. But this could not work for our data.
Best regards Sandra
-----Nachricht von greve@nmr.mgh.harvard.edu -----Datum: Fri, 28 Jun 2013 10:40:57 -0400 Von: Douglas N Greve greve@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] longitudinal analyses for one group An: freesurfer@nmr.mgh.harvard.edu
Hi Sandra, you cannot do the longitudinal statistical analysis in QDEC. You will have to use mri_glmfit. Look at the FSGD examples on the wiki. doug
On 06/28/2013 03:28 AM, Sandra Preissler wrote:
[Zitattext verstecken] Dear freesurfer experts,
we want to do longitudinal analyses for two different time points in only one group (We do not have a control group or different groups within the intervention). So we did the longitudinal processing as described in the tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#Prepar...).
Now we tried to investigate the results with Qdec. We wanted to test whether the averaged change of thickness between pre-test and post-test differs from zero. We had the experience that we could only test the averaged thickness by choosing a discrete factor in Qdec. Our Problem is that we don't have a control group. So we couldn't choose the group variable as discrete factor. It's an pre-post-design with only one group.
Is it possible to investigate changes in thickness between pre-test and post-test without choosing a factor? Or do we have to create a group variable as discrete factor?
Can you help us in fixing this problem?
Thanks in advance!
Sandra
This message was sent through https://webmail.uni-jena.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message was sent through https://webmail.uni-jena.de
Hallo Doug,
this one:
mri_glmfit --glmdir g1v2_I --y lh.g1v2_I.thickness.10.mgh --fsgd qdec/GLM/g1v2_I.fsgd --C qdec/GLM/main.mtx --C qdec/GLM/age.mtx --C qdec/GLM/Amputationsdauer.mtx
Sandra
Zitat von Douglas N Greve greve@nmr.mgh.harvard.edu:
Sandra, what was your final command line? doug
On 07/03/2013 06:28 AM, Sandra Preissler wrote:
Dear Doug,
Thanks a lot for your advice.
We followed the examples on the wiki (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#AssembletheDa...) and tried to analyze our data as described. We have a single group with two continuous covariates. Therefore we created the freesurfer descriptor file (g1v2_I.fsgd) and three contrast files (main.mtx; age.mtx; Amputationsdauer.mtx). The preprocessing finished without error for both hemispheres.
The following command line we used for the preprocessing: mris_preproc --fsgd qdec/GLM/g1v2_I.fsgd --cache-in long.thickness-avg.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.g1v2_I.thickness.10.mgh
After this we tried the mri_glmfit for our longitudinal data. Our command line was the following: mri_glmfit --glmdir g1v2_I --y lh.g1v2_I.thickness.10.mgh --fsgd qdec/GLM/g1v2_I.fsgd --C qdec/GLM/main.mtx --C qdec/GLM/age.mtx --C qdec/GLM/Amputationsdauer.mtx
We get the error message: ERROR: you must use '--surface subject hemi' with surface data
Therfore we tried to specify
subject as fsaverage, hemi as lh, surface as thickness.
Unfortunately, this did not work out and other alternative approaches to solve this problem did not function as well.
Do we have to create a subject descriptor file for our longitudinal templates? Or did we miss anything else? We thought about creating the --X «design matrix file» for longitudinal data, we found the instruction for between factors. But this could not work for our data.
Best regards Sandra
-----Nachricht von greve@nmr.mgh.harvard.edu -----Datum: Fri, 28 Jun 2013 10:40:57 -0400 Von: Douglas N Greve greve@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] longitudinal analyses for one group An: freesurfer@nmr.mgh.harvard.edu
Hi Sandra, you cannot do the longitudinal statistical analysis in QDEC. You will have to use mri_glmfit. Look at the FSGD examples on the wiki. doug
On 06/28/2013 03:28 AM, Sandra Preissler wrote:
[Zitattext verstecken] Dear freesurfer experts,
we want to do longitudinal analyses for two different time points in only one group (We do not have a control group or different groups within the intervention). So we did the longitudinal processing as described in the tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#Prepar...). Now we tried to investigate the results with Qdec. We wanted to test whether the averaged change of thickness between pre-test and post-test differs from zero. We had the experience that we could only test the averaged thickness by choosing a discrete factor in Qdec. Our Problem is that we don't have a control group. So we couldn't choose the group variable as discrete factor. It's an pre-post-design with only one group.
Is it possible to investigate changes in thickness between pre-test and post-test without choosing a factor? Or do we have to create a group variable as discrete factor?
Can you help us in fixing this problem?
Thanks in advance!
Sandra
This message was sent through https://webmail.uni-jena.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message was sent through https://webmail.uni-jena.de
-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
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you will need to add --surface fsaverage lh doug
On 07/03/2013 11:39 AM, Sandra Preissler wrote:
Hallo Doug,
this one:
mri_glmfit --glmdir g1v2_I --y lh.g1v2_I.thickness.10.mgh --fsgd qdec/GLM/g1v2_I.fsgd --C qdec/GLM/main.mtx --C qdec/GLM/age.mtx --C qdec/GLM/Amputationsdauer.mtx
Sandra
Zitat von Douglas N Greve greve@nmr.mgh.harvard.edu:
Sandra, what was your final command line? doug
On 07/03/2013 06:28 AM, Sandra Preissler wrote:
Dear Doug,
Thanks a lot for your advice.
We followed the examples on the wiki (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#AssembletheDa...) and tried to analyze our data as described. We have a single group with two continuous covariates. Therefore we created the freesurfer descriptor file (g1v2_I.fsgd) and three contrast files (main.mtx; age.mtx; Amputationsdauer.mtx). The preprocessing finished without error for both hemispheres.
The following command line we used for the preprocessing: mris_preproc --fsgd qdec/GLM/g1v2_I.fsgd --cache-in long.thickness-avg.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.g1v2_I.thickness.10.mgh
After this we tried the mri_glmfit for our longitudinal data. Our command line was the following: mri_glmfit --glmdir g1v2_I --y lh.g1v2_I.thickness.10.mgh --fsgd qdec/GLM/g1v2_I.fsgd --C qdec/GLM/main.mtx --C qdec/GLM/age.mtx --C qdec/GLM/Amputationsdauer.mtx
We get the error message: ERROR: you must use '--surface subject hemi' with surface data
Therfore we tried to specify
subject as fsaverage, hemi as lh, surface as thickness.
Unfortunately, this did not work out and other alternative approaches to solve this problem did not function as well.
Do we have to create a subject descriptor file for our longitudinal templates? Or did we miss anything else? We thought about creating the --X «design matrix file» for longitudinal data, we found the instruction for between factors. But this could not work for our data.
Best regards Sandra
-----Nachricht von greve@nmr.mgh.harvard.edu -----Datum: Fri, 28 Jun 2013 10:40:57 -0400 Von: Douglas N Greve greve@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] longitudinal analyses for one group An: freesurfer@nmr.mgh.harvard.edu
Hi Sandra, you cannot do the longitudinal statistical analysis in QDEC. You will have to use mri_glmfit. Look at the FSGD examples on the wiki. doug
On 06/28/2013 03:28 AM, Sandra Preissler wrote:
[Zitattext verstecken] Dear freesurfer experts,
we want to do longitudinal analyses for two different time points in only one group (We do not have a control group or different groups within the intervention). So we did the longitudinal processing as described in the tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#Prepar...). Now we tried to investigate the results with Qdec. We wanted to test whether the averaged change of thickness between pre-test and post-test differs from zero. We had the experience that we could only test the averaged thickness by choosing a discrete factor in Qdec. Our Problem is that we don't have a control group. So we couldn't choose the group variable as discrete factor. It's an pre-post-design with only one group.
Is it possible to investigate changes in thickness between pre-test and post-test without choosing a factor? Or do we have to create a group variable as discrete factor?
Can you help us in fixing this problem?
Thanks in advance!
Sandra
This message was sent through https://webmail.uni-jena.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message was sent through https://webmail.uni-jena.de
-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
This message was sent through https://webmail.uni-jena.de
Thank you so much!! It works!
sandra
Zitat von Douglas N Greve greve@nmr.mgh.harvard.edu:
you will need to add --surface fsaverage lh doug
On 07/03/2013 11:39 AM, Sandra Preissler wrote:
Hallo Doug,
this one:
mri_glmfit --glmdir g1v2_I --y lh.g1v2_I.thickness.10.mgh --fsgd qdec/GLM/g1v2_I.fsgd --C qdec/GLM/main.mtx --C qdec/GLM/age.mtx --C qdec/GLM/Amputationsdauer.mtx
Sandra
Zitat von Douglas N Greve greve@nmr.mgh.harvard.edu:
Sandra, what was your final command line? doug
On 07/03/2013 06:28 AM, Sandra Preissler wrote:
Dear Doug,
Thanks a lot for your advice.
We followed the examples on the wiki (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#AssembletheDa...) and tried to analyze our data as described. We have a single group with two continuous covariates. Therefore we created the freesurfer descriptor file (g1v2_I.fsgd) and three contrast files (main.mtx; age.mtx; Amputationsdauer.mtx). The preprocessing finished without error for both hemispheres.
The following command line we used for the preprocessing: mris_preproc --fsgd qdec/GLM/g1v2_I.fsgd --cache-in long.thickness-avg.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.g1v2_I.thickness.10.mgh
After this we tried the mri_glmfit for our longitudinal data. Our command line was the following: mri_glmfit --glmdir g1v2_I --y lh.g1v2_I.thickness.10.mgh --fsgd qdec/GLM/g1v2_I.fsgd --C qdec/GLM/main.mtx --C qdec/GLM/age.mtx --C qdec/GLM/Amputationsdauer.mtx
We get the error message: ERROR: you must use '--surface subject hemi' with surface data
Therfore we tried to specify
subject as fsaverage, hemi as lh, surface as thickness.
Unfortunately, this did not work out and other alternative approaches to solve this problem did not function as well.
Do we have to create a subject descriptor file for our longitudinal templates? Or did we miss anything else? We thought about creating the --X «design matrix file» for longitudinal data, we found the instruction for between factors. But this could not work for our data.
Best regards Sandra
-----Nachricht von greve@nmr.mgh.harvard.edu -----Datum: Fri, 28 Jun 2013 10:40:57 -0400 Von: Douglas N Greve greve@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] longitudinal analyses for one group An: freesurfer@nmr.mgh.harvard.edu
Hi Sandra, you cannot do the longitudinal statistical analysis in QDEC. You will have to use mri_glmfit. Look at the FSGD examples on the wiki. doug
On 06/28/2013 03:28 AM, Sandra Preissler wrote:
[Zitattext verstecken] Dear freesurfer experts,
we want to do longitudinal analyses for two different time points in only one group (We do not have a control group or different groups within the intervention). So we did the longitudinal processing as described in the tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#Prepar...). Now we tried to investigate the results with Qdec. We wanted to test whether the averaged change of thickness between pre-test and post-test differs from zero. We had the experience that we could only test the averaged thickness by choosing a discrete factor in Qdec. Our Problem is that we don't have a control group. So we couldn't choose the group variable as discrete factor. It's an pre-post-design with only one group.
Is it possible to investigate changes in thickness between pre-test and post-test without choosing a factor? Or do we have to create a group variable as discrete factor?
Can you help us in fixing this problem?
Thanks in advance!
Sandra
This message was sent through https://webmail.uni-jena.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message was sent through https://webmail.uni-jena.de
-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
This message was sent through https://webmail.uni-jena.de
-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Sandra Preissler