Hello Freesurfer group, I have a couple of questions - I'm using FreeSurfer 4.0.3 to recon-all my data. I've started using Qdec and I realized that it won't accept more that 4 variables to be selected. I would like diagnosis to be my main variable and then age, gender, and scanner version as covariates.
Do you know if there is a different version of Qdec that would allow me to do that analysis and if it is a problem to use data processed with a different prior version with it?
Thanks, Vina
Vina,
Qdec still doesnt support more than four variables, but you can still do the analysis by manually creating the input files to mri_glmfit by following this tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Nick
On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote:
Hello Freesurfer group, I have a couple of questions - I'm using FreeSurfer 4.0.3 to recon-all my data. I've started using Qdec and I realized that it won't accept more that 4 variables to be selected. I would like diagnosis to be my main variable and then age, gender, and scanner version as covariates.
Do you know if there is a different version of Qdec that would allow me to do that analysis and if it is a problem to use data processed with a different prior version with it?
Thanks, Vina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Nick. Would coding the data by elements/label GroupGenderHandedness be equivalent to looking at group effect and then covarying for gender and handedness?
Thanks!
Nick Schmansky wrote:
Vina,
Qdec still doesnt support more than four variables, but you can still do the analysis by manually creating the input files to mri_glmfit by following this tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Nick
On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote:
Hello Freesurfer group, I have a couple of questions - I'm using FreeSurfer 4.0.3 to recon-all my data. I've started using Qdec and I realized that it won't accept more that 4 variables to be selected. I would like diagnosis to be my main variable and then age, gender, and scanner version as covariates.
Do you know if there is a different version of Qdec that would allow me to do that analysis and if it is a problem to use data processed with a different prior version with it?
Thanks, Vina
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
Vina, there's an example here which is pretty close to what you are asking https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Vina Goghari wrote:
Thanks Nick. Would coding the data by elements/label GroupGenderHandedness be equivalent to looking at group effect and then covarying for gender and handedness?
Thanks!
Nick Schmansky wrote:
Vina,
Qdec still doesnt support more than four variables, but you can still do the analysis by manually creating the input files to mri_glmfit by following this tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Nick
On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote:
Hello Freesurfer group, I have a couple of questions - I'm using FreeSurfer 4.0.3 to recon-all my data. I've started using Qdec and I realized that it won't accept more that 4 variables to be selected. I would like diagnosis to be my main variable and then age, gender, and scanner version as covariates.
Do you know if there is a different version of Qdec that would allow me to do that analysis and if it is a problem to use data processed with a different prior version with it?
Thanks, Vina
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello, I have been trying to follow FreeSurfer guidelines to set up the analysis. I keep getting an error that I'm not sure what I did wrong. If you could take a quick look that would be great! I have qcached the data and run mri-preproc.
mri_glmfit \
--y lh.MERIT_sMRI.thickness.10.mgh \
--fsgd MERIT_sMRI.fsgd dods\
--C lh-con-rel.mtx \
--surf fsaverage lh \
--cortex \
--glmdir MERIT_sMRI.glmdir
This is my error:
shell loop% --y lh.MERIT_sMRI.thickness.10.mgh \ shell loop% --fsgd MERIT_sMRI.fsgd dods\ shell loop% --C lh-con-rel.mtx \ shell loop% --surf fsaverage lh \ shell loop% --cortex \ shell loop% --glmdir MERIT-sMRI.glmdir gdfReadHeader: reading MERIT_sMRI.fsgd INFO: ignoring tag Variable ERROR: gdfReadV1: Input line 1, subjid = MERIT_001 Found 3 variables, expected. 0 FSGDF Format Error: file = MERIT_sMRI.fsgd, tag=Input
Thanks so much!
Douglas N Greve wrote:
Vina, there's an example here which is pretty close to what you are asking https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Vina Goghari wrote:
Thanks Nick. Would coding the data by elements/label GroupGenderHandedness be equivalent to looking at group effect and then covarying for gender and handedness?
Thanks!
Nick Schmansky wrote:
Vina,
Qdec still doesnt support more than four variables, but you can still do the analysis by manually creating the input files to mri_glmfit by following this tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Nick
On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote:
Hello Freesurfer group, I have a couple of questions - I'm using FreeSurfer 4.0.3 to recon-all my data. I've started using Qdec and I realized that it won't accept more that 4 variables to be selected. I would like diagnosis to be my main variable and then age, gender, and scanner version as covariates.
Do you know if there is a different version of Qdec that would allow me to do that analysis and if it is a problem to use data processed with a different prior version with it?
Thanks, Vina
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
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
GroupDescriptorFile 1 Title MERIT_data Class Scz Class Rel Class Con Variable Age Gender Scanner Input MERIT_001 Con 25 1 1 Input MERIT_002 Rel 46 1 1 Input MERIT_003 Scz 50 1 1 Input MERIT_004 Rel 40 1 1 Input MERIT_005 Scz 49 2 1 Input MERIT_006 Rel 43 2 1 Input MERIT_007 Scz 28 1 1 Input MERIT_008 Con 22 1 1 Input MERIT_009 Con 42 2 1 Input MERIT_010 Con 55 1 1 Input MERIT_011 Scz 39 1 1 Input MERIT_012 Rel 47 1 1 Input MERIT_013 Rel 49 1 1 Input MERIT_015 Scz 49 1 1 Input MERIT_016 Rel 53 2 1 Input MERIT_017 Scz 58 2 1 Input MERIT_018 Con 48 1 1 Input MERIT_019 Scz 43 1 1 Input MERIT_020 Rel 58 2 1 Input MERIT_022 Scz 52 1 1 Input MERIT_023 Rel 53 2 1 Input MERIT_024 Con 49 1 1 Input MERIT_025 Scz 53 1 1 Input MERIT_026 Con 21 2 1 Input MERIT_027 Con 35 2 1 Input MERIT_028 Con 38 2 1 Input MERIT_029 Con 32 1 1 Input MERIT_030 Con 30 2 1 Input MERIT_031 Rel 57 1 1 Input MERIT_032 Con 26 2 1 Input MERIT_033 Con 32 2 1 Input MERIT_034 Scz 33 1 1 Input MERIT_035 Con 42 1 1 Input MERIT_036 Rel 55 2 1 Input MERIT_037 Rel 56 1 1 Input MERIT_038 Scz 36 2 1 Input MERIT_039 Con 47 1 1 Input MERIT_040 Scz 28 1 1 Input MERIT_041 Scz 42 1 1 Input MERIT_043 Scz 52 1 2 Input MERIT_044 Rel 31 2 2 Input MERIT_045 Rel 43 2 2 Input MERIT_046 Scz 41 1 2 Input MERIT_047 Scz 51 1 2 Input MERIT_048 Con 27 2 2 Input MERIT_049 Rel 48 2 2 Input MERIT_050 Scz 42 1 2 Input MERIT_051 Scz 30 1 2 Input MERIT_052 Scz 49 1 2 Input MERIT_053 Scz 54 2 2 Input MERIT_054 Rel 58 2 2 Input MERIT_055 Con 42 1 2 Input MERIT_056 Scz 58 1 2 Input MERIT_057 Con 27 1 2 Input MERIT_058 Scz 44 2 2 Input MERIT_059 Con 23 1 2 Input MERIT_060 Scz 59 1 2 Input MERIT_061 Con 58 1 2 Input MERIT_062 Con 49 2 2 Input MERIT_063 Scz 35 2 2 Input MERIT_064 Con 44 2 2 Input MERIT_065 Con 44 2 2 Input MERIT_067 Scz 40 1 2 Input MERIT_068 Rel 55 2 2 Input MERIT_069 Con 53 1 2 Input MERIT_070 Rel 53 2 2 Input MERIT_071 Con 50 2 2 Input MERIT_072 Rel 51 1 2 Input MERIT_073 Con 49 2 2 Input MERIT_074 Scz 22 1 2 Input MERIT_075 Rel 52 2 2 Input MERIT_076 Rel 44 2 2 Input MERIT_077 Scz 36 1 2 Input MERIT_078 Con 56 1 2 Input MERIT_079 Con 59 2 2 Input MERIT_080 Con 52 1 2 Input MERIT_081 Con 47 2 2 Input MERIT_082 Con 53 1 2 Input MERIT_083 Con 52 1 2 Input MERIT_084 Rel 50 2 2 Input MERIT_085 Rel 53 2 2 Input MERIT_086 Con 51 1 2 Input MERIT_087 Con 40 1 2 Input MERIT_088 Con 57 1 2 Input MERIT_089 Con 40 2 2 Input MERIT_090 Rel 50 1 2
did you declare the variables in the fsgd file? See the examples in the link below.
doug
Vina Goghari wrote:
Hello, I have been trying to follow FreeSurfer guidelines to set up the analysis. I keep getting an error that I'm not sure what I did wrong. If you could take a quick look that would be great! I have qcached the data and run mri-preproc.
mri_glmfit \
--y lh.MERIT_sMRI.thickness.10.mgh \
--fsgd MERIT_sMRI.fsgd dods\
--C lh-con-rel.mtx \
--surf fsaverage lh \
--cortex \
--glmdir MERIT_sMRI.glmdir
This is my error:
shell loop% --y lh.MERIT_sMRI.thickness.10.mgh \ shell loop% --fsgd MERIT_sMRI.fsgd dods\ shell loop% --C lh-con-rel.mtx \ shell loop% --surf fsaverage lh \ shell loop% --cortex \ shell loop% --glmdir MERIT-sMRI.glmdir gdfReadHeader: reading MERIT_sMRI.fsgd INFO: ignoring tag Variable ERROR: gdfReadV1: Input line 1, subjid = MERIT_001 Found 3 variables, expected. 0 FSGDF Format Error: file = MERIT_sMRI.fsgd, tag=Input
Thanks so much!
Douglas N Greve wrote:
Vina, there's an example here which is pretty close to what you are asking https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Vina Goghari wrote:
Thanks Nick. Would coding the data by elements/label GroupGenderHandedness be equivalent to looking at group effect and then covarying for gender and handedness?
Thanks!
Nick Schmansky wrote:
Vina,
Qdec still doesnt support more than four variables, but you can still do the analysis by manually creating the input files to mri_glmfit by following this tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Nick
On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote:
Hello Freesurfer group, I have a couple of questions - I'm using FreeSurfer 4.0.3 to recon-all my data. I've started using Qdec and I realized that it won't accept more that 4 variables to be selected. I would like diagnosis to be my main variable and then age, gender, and scanner version as covariates.
Do you know if there is a different version of Qdec that would allow me to do that analysis and if it is a problem to use data processed with a different prior version with it?
Thanks, Vina
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
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
Yes I have a Variable line: "Variable Age Sex Scanner," before I list all the Inputs.
Douglas N Greve wrote:
did you declare the variables in the fsgd file? See the examples in the link below.
doug
Vina Goghari wrote:
Hello, I have been trying to follow FreeSurfer guidelines to set up the analysis. I keep getting an error that I'm not sure what I did wrong. If you could take a quick look that would be great! I have qcached the data and run mri-preproc.
mri_glmfit \
--y lh.MERIT_sMRI.thickness.10.mgh \
--fsgd MERIT_sMRI.fsgd dods\
--C lh-con-rel.mtx \
--surf fsaverage lh \
--cortex \
--glmdir MERIT_sMRI.glmdir
This is my error:
shell loop% --y lh.MERIT_sMRI.thickness.10.mgh \ shell loop% --fsgd MERIT_sMRI.fsgd dods\ shell loop% --C lh-con-rel.mtx \ shell loop% --surf fsaverage lh \ shell loop% --cortex \ shell loop% --glmdir MERIT-sMRI.glmdir gdfReadHeader: reading MERIT_sMRI.fsgd INFO: ignoring tag Variable ERROR: gdfReadV1: Input line 1, subjid = MERIT_001 Found 3 variables, expected. 0 FSGDF Format Error: file = MERIT_sMRI.fsgd, tag=Input
Thanks so much!
Douglas N Greve wrote:
Vina, there's an example here which is pretty close to what you are asking https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Vina Goghari wrote:
Thanks Nick. Would coding the data by elements/label GroupGenderHandedness be equivalent to looking at group effect and then covarying for gender and handedness?
Thanks!
Nick Schmansky wrote:
Vina,
Qdec still doesnt support more than four variables, but you can still do the analysis by manually creating the input files to mri_glmfit by following this tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Nick
On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote:
Hello Freesurfer group, I have a couple of questions - I'm using FreeSurfer 4.0.3 to recon-all my data. I've started using Qdec and I realized that it won't accept more that 4 variables to be selected. I would like diagnosis to be my main variable and then age, gender, and scanner version as covariates.
Do you know if there is a different version of Qdec that would allow me to do that analysis and if it is a problem to use data processed with a different prior version with it?
Thanks, Vina
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
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
GroupDescriptorFile 1 Title MERIT_data Class Scz Class Rel Class Con Variable Age Gender Scanner Input MERIT_001 Con 25 1 1 Input MERIT_002 Rel 46 1 1 Input MERIT_003 Scz 50 1 1 Input MERIT_004 Rel 40 1 1 Input MERIT_005 Scz 49 2 1 Input MERIT_006 Rel 43 2 1 Input MERIT_007 Scz 28 1 1 Input MERIT_008 Con 22 1 1 Input MERIT_009 Con 42 2 1 Input MERIT_010 Con 55 1 1 Input MERIT_011 Scz 39 1 1 Input MERIT_012 Rel 47 1 1 Input MERIT_013 Rel 49 1 1 Input MERIT_015 Scz 49 1 1 Input MERIT_016 Rel 53 2 1 Input MERIT_017 Scz 58 2 1 Input MERIT_018 Con 48 1 1 Input MERIT_019 Scz 43 1 1 Input MERIT_020 Rel 58 2 1 Input MERIT_022 Scz 52 1 1 Input MERIT_023 Rel 53 2 1 Input MERIT_024 Con 49 1 1 Input MERIT_025 Scz 53 1 1 Input MERIT_026 Con 21 2 1 Input MERIT_027 Con 35 2 1 Input MERIT_028 Con 38 2 1 Input MERIT_029 Con 32 1 1 Input MERIT_030 Con 30 2 1 Input MERIT_031 Rel 57 1 1 Input MERIT_032 Con 26 2 1 Input MERIT_033 Con 32 2 1 Input MERIT_034 Scz 33 1 1 Input MERIT_035 Con 42 1 1 Input MERIT_036 Rel 55 2 1 Input MERIT_037 Rel 56 1 1 Input MERIT_038 Scz 36 2 1 Input MERIT_039 Con 47 1 1 Input MERIT_040 Scz 28 1 1 Input MERIT_041 Scz 42 1 1 Input MERIT_043 Scz 52 1 2 Input MERIT_044 Rel 31 2 2 Input MERIT_045 Rel 43 2 2 Input MERIT_046 Scz 41 1 2 Input MERIT_047 Scz 51 1 2 Input MERIT_048 Con 27 2 2 Input MERIT_049 Rel 48 2 2 Input MERIT_050 Scz 42 1 2 Input MERIT_051 Scz 30 1 2 Input MERIT_052 Scz 49 1 2 Input MERIT_053 Scz 54 2 2 Input MERIT_054 Rel 58 2 2 Input MERIT_055 Con 42 1 2 Input MERIT_056 Scz 58 1 2 Input MERIT_057 Con 27 1 2 Input MERIT_058 Scz 44 2 2 Input MERIT_059 Con 23 1 2 Input MERIT_060 Scz 59 1 2 Input MERIT_061 Con 58 1 2 Input MERIT_062 Con 49 2 2 Input MERIT_063 Scz 35 2 2 Input MERIT_064 Con 44 2 2 Input MERIT_065 Con 44 2 2 Input MERIT_067 Scz 40 1 2 Input MERIT_068 Rel 55 2 2 Input MERIT_069 Con 53 1 2 Input MERIT_070 Rel 53 2 2 Input MERIT_071 Con 50 2 2 Input MERIT_072 Rel 51 1 2 Input MERIT_073 Con 49 2 2 Input MERIT_074 Scz 22 1 2 Input MERIT_075 Rel 52 2 2 Input MERIT_076 Rel 44 2 2 Input MERIT_077 Scz 36 1 2 Input MERIT_078 Con 56 1 2 Input MERIT_079 Con 59 2 2 Input MERIT_080 Con 52 1 2 Input MERIT_081 Con 47 2 2 Input MERIT_082 Con 53 1 2 Input MERIT_083 Con 52 1 2 Input MERIT_084 Rel 50 2 2 Input MERIT_085 Rel 53 2 2 Input MERIT_086 Con 51 1 2 Input MERIT_087 Con 40 1 2 Input MERIT_088 Con 57 1 2 Input MERIT_089 Con 40 2 2 Input MERIT_090 Rel 50 1 2
can you send the fsgd file?
Vina Goghari wrote:
Yes I have a Variable line: "Variable Age Sex Scanner," before I list all the Inputs.
Douglas N Greve wrote:
did you declare the variables in the fsgd file? See the examples in the link below.
doug
Vina Goghari wrote:
Hello, I have been trying to follow FreeSurfer guidelines to set up the analysis. I keep getting an error that I'm not sure what I did wrong. If you could take a quick look that would be great! I have qcached the data and run mri-preproc.
mri_glmfit \
--y lh.MERIT_sMRI.thickness.10.mgh \
--fsgd MERIT_sMRI.fsgd dods\
--C lh-con-rel.mtx \
--surf fsaverage lh \
--cortex \
--glmdir MERIT_sMRI.glmdir
This is my error:
shell loop% --y lh.MERIT_sMRI.thickness.10.mgh \ shell loop% --fsgd MERIT_sMRI.fsgd dods\ shell loop% --C lh-con-rel.mtx \ shell loop% --surf fsaverage lh \ shell loop% --cortex \ shell loop% --glmdir MERIT-sMRI.glmdir gdfReadHeader: reading MERIT_sMRI.fsgd INFO: ignoring tag Variable ERROR: gdfReadV1: Input line 1, subjid = MERIT_001 Found 3 variables, expected. 0 FSGDF Format Error: file = MERIT_sMRI.fsgd, tag=Input
Thanks so much!
Douglas N Greve wrote:
Vina, there's an example here which is pretty close to what you are asking https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Vina Goghari wrote:
Thanks Nick. Would coding the data by elements/label GroupGenderHandedness be equivalent to looking at group effect and then covarying for gender and handedness?
Thanks!
Nick Schmansky wrote:
Vina,
Qdec still doesnt support more than four variables, but you can still do the analysis by manually creating the input files to mri_glmfit by following this tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Nick
On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote:
> Hello Freesurfer group, > I have a couple of questions - I'm using FreeSurfer 4.0.3 to > recon-all my data. I've started using Qdec and I realized that > it won't accept more that 4 variables to be selected. I would > like diagnosis to be my main variable and then age, gender, and > scanner version as covariates. > > Do you know if there is a different version of Qdec that would > allow me to do that analysis and if it is a problem to use data > processed with a different prior version with it? > > Thanks, > Vina > > _______________________________________________ > 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
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
Yes. Attached. Thanks!
Douglas N Greve wrote:
can you send the fsgd file?
Vina Goghari wrote:
Yes I have a Variable line: "Variable Age Sex Scanner," before I list all the Inputs.
Douglas N Greve wrote:
did you declare the variables in the fsgd file? See the examples in the link below.
doug
Vina Goghari wrote:
Hello, I have been trying to follow FreeSurfer guidelines to set up the analysis. I keep getting an error that I'm not sure what I did wrong. If you could take a quick look that would be great! I have qcached the data and run mri-preproc.
mri_glmfit \
--y lh.MERIT_sMRI.thickness.10.mgh \
--fsgd MERIT_sMRI.fsgd dods\
--C lh-con-rel.mtx \
--surf fsaverage lh \
--cortex \
--glmdir MERIT_sMRI.glmdir
This is my error:
shell loop% --y lh.MERIT_sMRI.thickness.10.mgh \ shell loop% --fsgd MERIT_sMRI.fsgd dods\ shell loop% --C lh-con-rel.mtx \ shell loop% --surf fsaverage lh \ shell loop% --cortex \ shell loop% --glmdir MERIT-sMRI.glmdir gdfReadHeader: reading MERIT_sMRI.fsgd INFO: ignoring tag Variable ERROR: gdfReadV1: Input line 1, subjid = MERIT_001 Found 3 variables, expected. 0 FSGDF Format Error: file = MERIT_sMRI.fsgd, tag=Input
Thanks so much!
Douglas N Greve wrote:
Vina, there's an example here which is pretty close to what you are asking https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Vina Goghari wrote:
Thanks Nick. Would coding the data by elements/label GroupGenderHandedness be equivalent to looking at group effect and then covarying for gender and handedness?
Thanks!
Nick Schmansky wrote:
> Vina, > > Qdec still doesnt support more than four variables, but you can > still do > the analysis by manually creating the input files to mri_glmfit by > following this tutorial: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > Nick > > > On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote: > > >> Hello Freesurfer group, >> I have a couple of questions - I'm using FreeSurfer 4.0.3 to >> recon-all my data. I've started using Qdec and I realized that >> it won't accept more that 4 variables to be selected. I would >> like diagnosis to be my main variable and then age, gender, and >> scanner version as covariates. >> >> Do you know if there is a different version of Qdec that would >> allow me to do that analysis and if it is a problem to use data >> processed with a different prior version with it? >> >> Thanks, >> Vina >> >> _______________________________________________ >> 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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GroupDescriptorFile 1 Title MERIT_data Class Scz Class Rel Class Con Variable Age Gender Scanner Input MERIT_001 Con 25 1 1 Input MERIT_002 Rel 46 1 1 Input MERIT_003 Scz 50 1 1 Input MERIT_004 Rel 40 1 1 Input MERIT_005 Scz 49 2 1 Input MERIT_006 Rel 43 2 1 Input MERIT_007 Scz 28 1 1 Input MERIT_008 Con 22 1 1 Input MERIT_009 Con 42 2 1 Input MERIT_010 Con 55 1 1 Input MERIT_011 Scz 39 1 1 Input MERIT_012 Rel 47 1 1 Input MERIT_013 Rel 49 1 1 Input MERIT_015 Scz 49 1 1 Input MERIT_016 Rel 53 2 1 Input MERIT_017 Scz 58 2 1 Input MERIT_018 Con 48 1 1 Input MERIT_019 Scz 43 1 1 Input MERIT_020 Rel 58 2 1 Input MERIT_022 Scz 52 1 1 Input MERIT_023 Rel 53 2 1 Input MERIT_024 Con 49 1 1 Input MERIT_025 Scz 53 1 1 Input MERIT_026 Con 21 2 1 Input MERIT_027 Con 35 2 1 Input MERIT_028 Con 38 2 1 Input MERIT_029 Con 32 1 1 Input MERIT_030 Con 30 2 1 Input MERIT_031 Rel 57 1 1 Input MERIT_032 Con 26 2 1 Input MERIT_033 Con 32 2 1 Input MERIT_034 Scz 33 1 1 Input MERIT_035 Con 42 1 1 Input MERIT_036 Rel 55 2 1 Input MERIT_037 Rel 56 1 1 Input MERIT_038 Scz 36 2 1 Input MERIT_039 Con 47 1 1 Input MERIT_040 Scz 28 1 1 Input MERIT_041 Scz 42 1 1 Input MERIT_043 Scz 52 1 2 Input MERIT_044 Rel 31 2 2 Input MERIT_045 Rel 43 2 2 Input MERIT_046 Scz 41 1 2 Input MERIT_047 Scz 51 1 2 Input MERIT_048 Con 27 2 2 Input MERIT_049 Rel 48 2 2 Input MERIT_050 Scz 42 1 2 Input MERIT_051 Scz 30 1 2 Input MERIT_052 Scz 49 1 2 Input MERIT_053 Scz 54 2 2 Input MERIT_054 Rel 58 2 2 Input MERIT_055 Con 42 1 2 Input MERIT_056 Scz 58 1 2 Input MERIT_057 Con 27 1 2 Input MERIT_058 Scz 44 2 2 Input MERIT_059 Con 23 1 2 Input MERIT_060 Scz 59 1 2 Input MERIT_061 Con 58 1 2 Input MERIT_062 Con 49 2 2 Input MERIT_063 Scz 35 2 2 Input MERIT_064 Con 44 2 2 Input MERIT_065 Con 44 2 2 Input MERIT_067 Scz 40 1 2 Input MERIT_068 Rel 55 2 2 Input MERIT_069 Con 53 1 2 Input MERIT_070 Rel 53 2 2 Input MERIT_071 Con 50 2 2 Input MERIT_072 Rel 51 1 2 Input MERIT_073 Con 49 2 2 Input MERIT_074 Scz 22 1 2 Input MERIT_075 Rel 52 2 2 Input MERIT_076 Rel 44 2 2 Input MERIT_077 Scz 36 1 2 Input MERIT_078 Con 56 1 2 Input MERIT_079 Con 59 2 2 Input MERIT_080 Con 52 1 2 Input MERIT_081 Con 47 2 2 Input MERIT_082 Con 53 1 2 Input MERIT_083 Con 52 1 2 Input MERIT_084 Rel 50 2 2 Input MERIT_085 Rel 53 2 2 Input MERIT_086 Con 51 1 2 Input MERIT_087 Con 40 1 2 Input MERIT_088 Con 57 1 2 Input MERIT_089 Con 40 2 2 Input MERIT_090 Rel 50 1 2
ah, the line should read "Variables" not "Variable"
doug
Vina Goghari wrote:
Yes. Attached. Thanks!
Douglas N Greve wrote:
can you send the fsgd file?
Vina Goghari wrote:
Yes I have a Variable line: "Variable Age Sex Scanner," before I list all the Inputs.
Douglas N Greve wrote:
did you declare the variables in the fsgd file? See the examples in the link below.
doug
Vina Goghari wrote:
Hello, I have been trying to follow FreeSurfer guidelines to set up the analysis. I keep getting an error that I'm not sure what I did wrong. If you could take a quick look that would be great! I have qcached the data and run mri-preproc.
mri_glmfit \
--y lh.MERIT_sMRI.thickness.10.mgh \
--fsgd MERIT_sMRI.fsgd dods\
--C lh-con-rel.mtx \
--surf fsaverage lh \
--cortex \
--glmdir MERIT_sMRI.glmdir
This is my error:
shell loop% --y lh.MERIT_sMRI.thickness.10.mgh \ shell loop% --fsgd MERIT_sMRI.fsgd dods\ shell loop% --C lh-con-rel.mtx \ shell loop% --surf fsaverage lh \ shell loop% --cortex \ shell loop% --glmdir MERIT-sMRI.glmdir gdfReadHeader: reading MERIT_sMRI.fsgd INFO: ignoring tag Variable ERROR: gdfReadV1: Input line 1, subjid = MERIT_001 Found 3 variables, expected. 0 FSGDF Format Error: file = MERIT_sMRI.fsgd, tag=Input
Thanks so much!
Douglas N Greve wrote:
Vina, there's an example here which is pretty close to what you are asking https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Vina Goghari wrote:
> Thanks Nick. Would coding the data by elements/label > GroupGenderHandedness be equivalent to looking at group effect > and then covarying for gender and handedness? > > Thanks! > > Nick Schmansky wrote: > >> Vina, >> >> Qdec still doesnt support more than four variables, but you can >> still do >> the analysis by manually creating the input files to mri_glmfit by >> following this tutorial: >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >> >> Nick >> >> >> On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote: >> >> >>> Hello Freesurfer group, >>> I have a couple of questions - I'm using FreeSurfer 4.0.3 to >>> recon-all my data. I've started using Qdec and I realized that >>> it won't accept more that 4 variables to be selected. I would >>> like diagnosis to be my main variable and then age, gender, >>> and scanner version as covariates. >>> >>> Do you know if there is a different version of Qdec that would >>> allow me to do that analysis and if it is a problem to use >>> data processed with a different prior version with it? >>> >>> Thanks, >>> Vina >>> >>> _______________________________________________ >>> 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 >> > > > > > _______________________________________________ > 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
Thanks for your help. I probably would not have seen that!
I have been working with 4.0.3 FreeSurfer. I don't think there is a mri_glmfit-sim, though it seems that there is a --sim function for mri_glmfit-sim. I'm have trouble figuring out what the code would be exactly to run it.
Alternatively I can just down load the newer version and use that with my processed 4.03 data?
Thanks!!!
Douglas N Greve wrote:
ah, the line should read "Variables" not "Variable"
doug
Vina Goghari wrote:
Yes. Attached. Thanks!
Douglas N Greve wrote:
can you send the fsgd file?
Vina Goghari wrote:
Yes I have a Variable line: "Variable Age Sex Scanner," before I list all the Inputs.
Douglas N Greve wrote:
did you declare the variables in the fsgd file? See the examples in the link below.
doug
Vina Goghari wrote:
Hello, I have been trying to follow FreeSurfer guidelines to set up the analysis. I keep getting an error that I'm not sure what I did wrong. If you could take a quick look that would be great! I have qcached the data and run mri-preproc.
mri_glmfit \
--y lh.MERIT_sMRI.thickness.10.mgh \
--fsgd MERIT_sMRI.fsgd dods\
--C lh-con-rel.mtx \
--surf fsaverage lh \
--cortex \
--glmdir MERIT_sMRI.glmdir
This is my error:
shell loop% --y lh.MERIT_sMRI.thickness.10.mgh \ shell loop% --fsgd MERIT_sMRI.fsgd dods\ shell loop% --C lh-con-rel.mtx \ shell loop% --surf fsaverage lh \ shell loop% --cortex \ shell loop% --glmdir MERIT-sMRI.glmdir gdfReadHeader: reading MERIT_sMRI.fsgd INFO: ignoring tag Variable ERROR: gdfReadV1: Input line 1, subjid = MERIT_001 Found 3 variables, expected. 0 FSGDF Format Error: file = MERIT_sMRI.fsgd, tag=Input
Thanks so much!
Douglas N Greve wrote:
> > Vina, there's an example here which is pretty close to what you > are asking > https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > > Vina Goghari wrote: > >> Thanks Nick. Would coding the data by elements/label >> GroupGenderHandedness be equivalent to looking at group effect >> and then covarying for gender and handedness? >> >> Thanks! >> >> Nick Schmansky wrote: >> >>> Vina, >>> >>> Qdec still doesnt support more than four variables, but you >>> can still do >>> the analysis by manually creating the input files to >>> mri_glmfit by >>> following this tutorial: >>> >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >>> >>> Nick >>> >>> >>> On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote: >>> >>> >>>> Hello Freesurfer group, >>>> I have a couple of questions - I'm using FreeSurfer 4.0.3 to >>>> recon-all my data. I've started using Qdec and I realized >>>> that it won't accept more that 4 variables to be selected. I >>>> would like diagnosis to be my main variable and then age, >>>> gender, and scanner version as covariates. >>>> >>>> Do you know if there is a different version of Qdec that >>>> would allow me to do that analysis and if it is a problem to >>>> use data processed with a different prior version with it? >>>> >>>> Thanks, >>>> Vina >>>> >>>> _______________________________________________ >>>> 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 >>> >> >> >> >> >> _______________________________________________ >> 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
Vina,
Yes, you can download v4.2.0 and continue to use your v4.0.3 data (just dont mix running recon-all -all of future subjects using v4.2.0 with v4.0.3).
You can use the new mri_glmfit-sim utility with your v4.0.3 data.
Nick
On Tue, 2009-02-03 at 19:01 -0600, Vina Goghari wrote:
Thanks for your help. I probably would not have seen that!
I have been working with 4.0.3 FreeSurfer. I don't think there is a mri_glmfit-sim, though it seems that there is a --sim function for mri_glmfit-sim. I'm have trouble figuring out what the code would be exactly to run it.
Alternatively I can just down load the newer version and use that with my processed 4.03 data?
Thanks!!!
Douglas N Greve wrote:
ah, the line should read "Variables" not "Variable"
doug
Vina Goghari wrote:
Yes. Attached. Thanks!
Douglas N Greve wrote:
can you send the fsgd file?
Vina Goghari wrote:
Yes I have a Variable line: "Variable Age Sex Scanner," before I list all the Inputs.
Douglas N Greve wrote:
did you declare the variables in the fsgd file? See the examples in the link below.
doug
Vina Goghari wrote:
> Hello, > I have been trying to follow FreeSurfer guidelines to set up the > analysis. I keep getting an error that I'm not sure what I did > wrong. If you could take a quick look that would be great! I have > qcached the data and run mri-preproc. > > mri_glmfit \ > > --y lh.MERIT_sMRI.thickness.10.mgh \ > > --fsgd MERIT_sMRI.fsgd dods\ > > --C lh-con-rel.mtx \ > > --surf fsaverage lh \ > > --cortex \ > > --glmdir MERIT_sMRI.glmdir > > This is my error: > > shell loop% --y lh.MERIT_sMRI.thickness.10.mgh \ > shell loop% --fsgd MERIT_sMRI.fsgd dods\ > shell loop% --C lh-con-rel.mtx \ > shell loop% --surf fsaverage lh \ > shell loop% --cortex \ > shell loop% --glmdir MERIT-sMRI.glmdir > gdfReadHeader: reading MERIT_sMRI.fsgd > INFO: ignoring tag Variable > ERROR: gdfReadV1: Input line 1, subjid = MERIT_001 > Found 3 variables, expected. 0 > FSGDF Format Error: file = MERIT_sMRI.fsgd, tag=Input > > Thanks so much! > > Douglas N Greve wrote: > >> >> Vina, there's an example here which is pretty close to what you >> are asking >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples >> >> Vina Goghari wrote: >> >>> Thanks Nick. Would coding the data by elements/label >>> GroupGenderHandedness be equivalent to looking at group effect >>> and then covarying for gender and handedness? >>> >>> Thanks! >>> >>> Nick Schmansky wrote: >>> >>>> Vina, >>>> >>>> Qdec still doesnt support more than four variables, but you >>>> can still do >>>> the analysis by manually creating the input files to >>>> mri_glmfit by >>>> following this tutorial: >>>> >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >>>> >>>> Nick >>>> >>>> >>>> On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote: >>>> >>>> >>>>> Hello Freesurfer group, >>>>> I have a couple of questions - I'm using FreeSurfer 4.0.3 to >>>>> recon-all my data. I've started using Qdec and I realized >>>>> that it won't accept more that 4 variables to be selected. I >>>>> would like diagnosis to be my main variable and then age, >>>>> gender, and scanner version as covariates. >>>>> >>>>> Do you know if there is a different version of Qdec that >>>>> would allow me to do that analysis and if it is a problem to >>>>> use data processed with a different prior version with it? >>>>> >>>>> Thanks, >>>>> Vina >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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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