[Freesurfer] FDR correction
External Email - Use Caution Hi, I performed an statistical analysis comparing autism group with control group using volume/area and thickness measures. I found significant differences in some regions but they were not significant after FDR correction. The majority of p-values are really high and only some of them are small, I would like to know is that can affect the result. Additionally, I read that it is interesting to do a power analysis to know the amount of difference that can be detected based on the sample size and I would like to know if it is a good approach to follow trying to explain why some results were not significant after multiple comparison correction. Thank you, Laura ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Power analysis
External Email - Use Caution Hi, I want to perform a power analysis and I read that I need 3 of 4 things: 1. Effect size (mean/std) 2. False positive rate 3. Number of subjects 4. True positive rate I also read that the effect size can be calculated using gamma.mgh and gammavar.mgh files but I do not know how to open them in order to get the numbers. Thank you, Laura ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Power analysis
External Email - Use Caution
Dear Douglas,
I performed the statistical analysis using stats files so I do not have vertex
information, I assume it will be cortical regions information. Is the approach
to read them the same?
Thank you,
Laura
> El 11 dic 2018, a las 16:54, Greve, Douglas N.,Ph.D.
> escribió:
>
> The gamma and gammavar files are vertex-wise values. You can load them
> in matlab with something like
> g = MRIread('gamma.mgh');
> gv = MRIread('gammavar.mgz');
> but you will need the vertex that you are interested in (or do for all
> vertices).
> You can use fast_glm_power.m in the FSFAST toolbox to compute the power
> (requires stats toolbox).
>
>
> On 12/11/18 6:39 AM, Laura Ferrero wrote:
>> External Email - Use Caution
>>
>> Hi,
>> I want to perform a power analysis and I read that I need 3 of 4 things:
>> 1. Effect size (mean/std)
>> 2. False positive rate
>> 3. Number of subjects
>> 4. True positive rate
>>
>> I also read that the effect size can be calculated using gamma.mgh and
>> gammavar.mgh files but I do not know how to open them in order to get the
>> numbers.
>>
>> Thank you,
>> Laura
>>
>> ___
>> 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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Re: [Freesurfer] Power analysis
External Email - Use Caution
After using MRIread from Matlab in file gamma.mgh, I obtain the following:
mri =
struct with fields:
srcbext: ''
analyzehdr: []
bhdr: []
vol: []
fspec: 'gamma.mgh'
pwd: '/Users/lauraferrero/Documents/MATLAB'
flip_angle: 0
tr: 0
te: 0
ti: 0
vox2ras0: [4×4 double]
volsize: [1 34 1]
height: 1
width: 34
depth: 1
nframes: 1
vox2ras: [4×4 double]
nvoxels: 34
xsize: 1
ysize: 1
zsize: 1
x_r: 1
x_a: 0
x_s: 0
y_r: 0
y_a: 1
y_s: 0
z_r: 0
z_a: 0
z_s: 1
c_r: 0
c_a: 0
c_s: 0
vox2ras1: [4×4 double]
Mdc: [3×3 double]
volres: [1 1 1]
tkrvox2ras: [4×4 double]
But I do not know which field corresponds to the mean for the effect size.
Regards,
Laura
> El 11 dic 2018, a las 18:21, Laura Ferrero
> escribió:
>
> Dear Douglas,
>
> I performed the statistical analysis using stats files so I do not have
> vertex information, I assume it will be cortical regions information. Is the
> approach to read them the same?
> Thank you,
> Laura
>
>
>
>
>> El 11 dic 2018, a las 16:54, Greve, Douglas N.,Ph.D.
>> escribió:
>>
>> The gamma and gammavar files are vertex-wise values. You can load them
>> in matlab with something like
>> g = MRIread('gamma.mgh');
>> gv = MRIread('gammavar.mgz');
>> but you will need the vertex that you are interested in (or do for all
>> vertices).
>> You can use fast_glm_power.m in the FSFAST toolbox to compute the power
>> (requires stats toolbox).
>>
>>
>> On 12/11/18 6:39 AM, Laura Ferrero wrote:
>>>External Email - Use Caution
>>>
>>> Hi,
>>> I want to perform a power analysis and I read that I need 3 of 4 things:
>>> 1. Effect size (mean/std)
>>> 2. False positive rate
>>> 3. Number of subjects
>>> 4. True positive rate
>>>
>>> I also read that the effect size can be calculated using gamma.mgh and
>>> gammavar.mgh files but I do not know how to open them in order to get the
>>> numbers.
>>>
>>> Thank you,
>>> Laura
>>>
>>> ___
>>> 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
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[Freesurfer] Power analysis
External Email - Use Caution I performed a two tailed t-test analysis using stats data and after the analysis, results were corrected for multiple comparisons using FDR. Now, I want to perform a power analysis and I have some doubts: 1. Gammavar is the variance or the standard deviation (i.e., effect size should be gamma/gammavar or gamma/sqrt(gammavar)). 2. The alpha value to be used should be the original alpha (0,05) or the new one obtained after FDR. Thank you, Laura ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Multiple comparisons
Dear FS team, I would like to correct for multiple comparisons after I run command-line GLM analysis on stats tables. I would like to make a second level analysis between a control group and an autism group. I would like to know if there is a command-line in FreeSurfer or if there is any program or toolkit in Matlab that allows to do that. Thank you, Laura ___ 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.
Re: [Freesurfer] Statistical analysis
Dear FS team, I would like to make an analysis between a Patients Group and a Control Group. This study is focused on identifying if there are differences in volume between both groups. I want to regress out the effects of gender, age and IQ. My designed matrix has the following structure: GroupDescriptorFile1 Class PatientMale Class PatientFemale Class ControlMale Class ControlFemale Variables Age IQ Input subject1 PatientMale 25 110 Input subject2 ControlMale 30 90 I was thinking about a Contrast Matrix like this: 0.5 0.5 -0.5-0.50 0 0 0 0 0 0 0 However, looking for some information I discovered that it only compares volume of two groups at the naissance because it is only comparing intercepts. Therefore, how I could make a comparison between volumes of two groups in general? Thank you, Laura ___ 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.
Re: [Freesurfer] Statistical analysis
In the case that exists an interaction between group and covariate. How a test comparing the mean volume of each group, like SPM does, could be done? I do not want to know if the different groups evolve in a different way with covariates, I only want to compare if groups have different volume in some regions of the brain. Or FreeSurfer does not allow to do a comparison like that? Thank you Douglas Greve escribió: > You should first test whether there is an interaction between group and > covariate. If there is non, then you can keep the same FSGD file but run > it with DOSS (different offset, same slope). The "same slope" means that > the difference will be the same regardless of the value of the > covariate. You will need to make a different contrast. See > https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss > > for more info > > > On 4/16/17 7:04 AM, Laura Ferrero Montes wrote: >> >> >> Dear FS team, >> I would like to make an analysis between a Patients Group and a >> Control Group. This study is focused on identifying if there are >> differences in volume between both groups. I want to regress out the >> effects of gender, age and IQ. >> >> My designed matrix has the following structure: >> GroupDescriptorFile1 >> Class PatientMale >> Class PatientFemale >> Class ControlMale >> Class ControlFemale >> VariablesAge IQ >> Input subject1 PatientMale 25 110 >> Input subject2 ControlMale 30 90 >> >> I was thinking about a Contrast Matrix like this: >> 0.5 0.5 -0.5-0.50 0 0 0 0 0 >> 0 0 >> However, looking for some information I discovered that it only >> compares volume of two groups at the naissance because it is only >> comparing intercepts. Therefore, how I could make a comparison between >> volumes of two groups in general? >> Thank you, >> Laura >> >> >> >> ___ >> 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Statistical analysis
Dear FS team, Thank you very much for your help. Just a few more questions. I want to perform a statistical analysis between two groups:controls and patients, using age and IQ as covariates. First I have to test if there is an interaction between group and covariate using DODS. My questions are: Q1) Do I have to test age and IQ separately, or together? Q2) In case that there is not interaction in any of the covariates, can I use the same FSGD file but do I have tu run it as DOSS? How it could be done? I would appreciate if you could give me some hints or examples about the matrices and contrast files that I must use. Thank you, All the best, Laura ___ 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] Statistical analysis
Dear FS team, Thank you very much for your help. Just a few more questions. I want to perform a statistical analysis between two groups:controls and patients, using age and IQ as covariates. First I have to test if there is an interaction between group and covariate using DODS. My questions are: Q1) Do I have to test age and IQ separately, or together? Q2) In case that there is not interaction in any of the covariates, can I use the same FSGD file but do I have tu run it as DOSS? How it could be done? I would appreciate if you could give me some hints or examples about the matrices and contrast files that I must use. Thank you, All the best, Laura ___ 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.
Re: [Freesurfer] Statistical analysis
Hi Joost, Thank you for the information, that course would be great. However, I would need to know if the analysis I am doing is OK to continue with my study. Joost Janssen escribió: > Hi Laura, > > There is an upcoming FreeSurfer course in Barcelona this summer. Please > contact Susana Carmona > susannacarm...@gmail.com > > Op 7 mei 2017 19:17 schreef "Laura Ferrero Montes" : > >> >> Dear FS team, >> >> Thank you very much for your help. Just a few more questions. >> >> I want to perform a statistical analysis between two groups:controls >> and patients, using age and IQ as covariates. First I have to test if >> there is an interaction between group and covariate using DODS. >> >> My questions are: >> >> Q1) Do I have to test age and IQ separately, or together? >> >> Q2) In case that there is not interaction in any of the covariates, >> can I use the same FSGD file but do I have tu run it as DOSS? How it >> could be done? >> I would appreciate if you could give me some hints or examples about >> the matrices and contrast files that I must use. >> >> Thank you, >> All the best, >> >> Laura >> ___ >> 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Multicenter studies
Dear FS team, In case I have data from different centers and I would like to do a group analysis between Patients and Controls, how different centers effects could be regressed out? Should I have to analyze if there is an interaction between center and group? I have seen examples of continuous variables and groups but not in the case of categorical ones. Thank you, Laura ___ 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.
Re: [Freesurfer] Multicenter studies
Thank you for the information. I just want to be sure if I have understood it properly. If I had two groups and two sites, my design matrix would be like: GroupDescriptorFile 1 Class PatientsGroup1 Class PatientsGroup2 Class ControlsGroup1 Class ControlsGroup2 If I want to test for the effect of group, contrast matrix would be: 0.5 -0.5 0.5 -0.5 If I want to test for the effect of site, contrast matrix would be: 0.5 0.5 -0.5 -0.5 Finally, in case of interaction test, how contrast matrix would be? Douglas N Greve escribió: > You should make sure to have a balanced design (ie, approx the same pats > and cons at each site). Then include site as a regressor, ie, if you had > two groups and two sites, you would have four regressors. You could > then test for the effect of group, the effect of site, and the > interaction. If there is an interaction, then it is hard to interpret > the differences between groups. > ___ 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] Error reading FSGD file
Dear FS team, I was trying to do an analylisis using mri_glmfit command. The analysis consists of two groups of patients and I wanted to know if there was an interaction between age and group. I wrote the following lines: mri_glmfit --table table1.txt --fsgd Descriptor.txt --C C1.txt --glmfir firstanalysis.glmdir - table1 was obtained afther command aparc2stats - C1 is the contrast matrix: 0 0 1 -1 0 0 - Descriptor.txt if the design matrix: GroupDescriptorFile 1 Title PatientsControls Class Patient Class Control Variables Age IQ Input NYU_0050985 Patient 13.09 90 Input NYU_0051099 Control 13.72 87 Input NYU_0051021 Patient 23.66 112 Input NYU_0051067 Control 23.65 116 Input NYU_0050996 Patient 15.81 100 Input NYU_0051104 Control 15.27 104 . . . I got this error: gdfRead(): reading Descriptor.txt ERROR: fio_FileHasCarriageReturn(): cannot open Descriptor.txt I created this matrix using text editor in Linux. Would yo know what is the problem? Thank you ___ 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] Multiple comparisons
Dear FS team, I was doing a statistical analysis using metrics that are provided in stats files like volume of different regions, so I am not doing a voxel based morphometry. It is necessary to correct for multiple comparisons or as I am only comparing the measures of the regions between to grups, it is not ? Thank you in advance ___ 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] aseg.stats
Dear FS team, I would like to obtain Total Brain Volume using metrics provided in aseg.stats. I have the idea of obtaining it as a result of white matter + grey matter. WM is provided in CorticalWhiteMatter and GM could be obtained with: TotalGreyMatter - RightCerebellumCortex - LeftCerebellumCortex. Would it be correct? Thank you ___ 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.
