Hello everyone,
Please pardon my rather simple question
I have done a GLM fit anlysis and have obtained a file sig.mgh alonf with a few others after the analysis.As I know, I do not have to create ROIs in order to do this. I also understand that doing a multiple comparison analysis just compares the regions of importance and evaluates them giving the most resilient cluster depending on the threshold. So, this does not give a thickness estimate. I would like to know how do I get the cortical thickness values from the results? If so, can I do it after glmfit?
And thanks Doug for your help in the other questions that I had prior to this!
Thank you
There should be a file called something like cache.th13.abs.y.ocn.dat. This will have a column for each cluster and a row for each subject. The value in the row will be the input for each subject. doug
On 05/30/2013 11:21 PM, Joshua deSouza wrote:
Hello everyone,
Please pardon my rather simple question
I have done a GLM fit anlysis and have obtained a file sig.mgh alonf with a few others after the analysis.As I know, I do not have to create ROIs in order to do this. I also understand that doing a multiple comparison analysis just compares the regions of importance and evaluates them giving the most resilient cluster depending on the threshold. So, this does not give a thickness estimate. I would like to know how do I get the cortical thickness values from the results? If so, can I do it after glmfit?
And thanks Doug for your help in the other questions that I had prior to this!
Thank you
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
This file that your saying, will be created after glmfit-sim is done using the cache function and a threshold of 1.3 and absolute ,with y being the fsgd file? Am I understanding this correctly?
Thank you
Joshua
On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
There should be a file called something like cache.th13.abs.y.ocn.dat. This will have a column for each cluster and a row for each subject. The value in the row will be the input for each subject. doug
On 05/30/2013 11:21 PM, Joshua deSouza wrote:
Hello everyone,
Please pardon my rather simple question
I have done a GLM fit anlysis and have obtained a file sig.mgh alonf with a few others after the analysis.As I know, I do not have to create ROIs in order to do this. I also understand that doing a multiple comparison analysis just compares the regions of importance and evaluates them giving the most resilient cluster depending on the threshold. So, this does not give a thickness estimate. I would like to know how do I get the cortical thickness values from the results? If so, can I do it after glmfit?
And thanks Doug for your help in the other questions that I had prior to this!
Thank you
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: 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/
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.
This file is always created by mri_glmfit-sim. It might be named something different depending on your parameters (should always end in y.ocn.dat) doug
On 6/2/13 3:57 AM, Joshua deSouza wrote:
Hi Doug,
This file that your saying, will be created after glmfit-sim is done using the cache function and a threshold of 1.3 and absolute ,with y being the fsgd file? Am I understanding this correctly?
Thank you
Joshua
On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
There should be a file called something like cache.th13.abs.y.ocn.dat. This will have a column for each cluster and a row for each subject. The value in the row will be the input for each subject. doug On 05/30/2013 11:21 PM, Joshua deSouza wrote: > Hello everyone, > > Please pardon my rather simple question > > I have done a GLM fit anlysis and have obtained a file sig.mgh alonf > with a few others after the analysis.As I know, I do not have to > create ROIs in order to do this. I also understand that doing a > multiple comparison analysis just compares the regions of importance > and evaluates them giving the most resilient cluster depending on the > threshold. So, this does not give a thickness estimate. I would like > to know how do I get the cortical thickness values from the results? > If so, can I do it after glmfit? > > And thanks Doug for your help in the other questions that I had prior > to this! > > Thank you > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Hello Doug,
Thank you for your quick replies to my queries. Really appreciate it.
I have found the files containing the cortical thickness values. Thank you. I assume that the order in which they follow are based on the fsgd file and the cluster annotation numbers.
I was just slightly confused about the residual fwhm. I have already done a smoothing of 15 on the file and have recieved a residual value of 47, which I assume is extremely large. Since I'm finding out values for the entire cortex I cannot do a glmfit-sim as there are no fwhm cache values of 47. Could you please tell me what the residual values mean? What do you recommend I do? Is there anything I can read up on to find out more about this? (Please pardon my questions if they seem a little trivial)
Thank you
Joshua
On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
This file is always created by mri_glmfit-sim. It might be named something different depending on your parameters (should always end in y.ocn.dat) doug
On 6/2/13 3:57 AM, Joshua deSouza wrote:
Hi Doug,
This file that your saying, will be created after glmfit-sim is done using the cache function and a threshold of 1.3 and absolute ,with y being the fsgd file? Am I understanding this correctly?
Thank you
Joshua
On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
There should be a file called something like cache.th13.abs.y.ocn.dat. This will have a column for each cluster and a row for each subject. The value in the row will be the input for each subject. doug
On 05/30/2013 11:21 PM, Joshua deSouza wrote:
Hello everyone,
Please pardon my rather simple question
I have done a GLM fit anlysis and have obtained a file sig.mgh alonf with a few others after the analysis.As I know, I do not have to create ROIs in order to do this. I also understand that doing a multiple comparison analysis just compares the regions of importance and evaluates them giving the most resilient cluster depending on the threshold. So, this does not give a thickness estimate. I would like to know how do I get the cortical thickness values from the results? If so, can I do it after glmfit?
And thanks Doug for your help in the other questions that I had prior to this!
Thank you
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: 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/
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.
The residual FWHM is measured from the data itself. You apply a certain amount of smoothing, but there is already some smoothness to the data, so the final fwhm is a combination of what is already there and what you apply. A fwhm of 47 is huge and may indicate that something is wrong. What is the input? cortical thickness? Are you using your own mask or is this a whole hemisphere analysis?
doug
On 6/2/13 10:29 PM, Joshua deSouza wrote:
Hello Doug,
Thank you for your quick replies to my queries. Really appreciate it.
I have found the files containing the cortical thickness values. Thank you. I assume that the order in which they follow are based on the fsgd file and the cluster annotation numbers.
I was just slightly confused about the residual fwhm. I have already done a smoothing of 15 on the file and have recieved a residual value of 47, which I assume is extremely large. Since I'm finding out values for the entire cortex I cannot do a glmfit-sim as there are no fwhm cache values of 47. Could you please tell me what the residual values mean? What do you recommend I do? Is there anything I can read up on to find out more about this? (Please pardon my questions if they seem a little trivial)
Thank you
Joshua
On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
This file is always created by mri_glmfit-sim. It might be named something different depending on your parameters (should always end in y.ocn.dat) doug On 6/2/13 3:57 AM, Joshua deSouza wrote:Hi Doug, This file that your saying, will be created after glmfit-sim is done using the cache function and a threshold of 1.3 and absolute ,with y being the fsgd file? Am I understanding this correctly? Thank you Joshua On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: There should be a file called something like cache.th13.abs.y.ocn.dat. This will have a column for each cluster and a row for each subject. The value in the row will be the input for each subject. doug On 05/30/2013 11:21 PM, Joshua deSouza wrote: > Hello everyone, > > Please pardon my rather simple question > > I have done a GLM fit anlysis and have obtained a file sig.mgh alonf > with a few others after the analysis.As I know, I do not have to > create ROIs in order to do this. I also understand that doing a > multiple comparison analysis just compares the regions of importance > and evaluates them giving the most resilient cluster depending on the > threshold. So, this does not give a thickness estimate. I would like > to know how do I get the cortical thickness values from the results? > If so, can I do it after glmfit? > > And thanks Doug for your help in the other questions that I had prior > to this! > > Thank you > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 Doug,
The command line is mri_glmfit --y lh.t.15.mgh --fsgd t.txt dods --C t1.txt --surface fsaverage lh --cortex --fwhm 15 --glmdir lh.t.15.glmdir
I am doing a whole hemisphere analysis and am measuring cortical thickness. I do not have my own mask but I have doubts about the mask that has been produced because from previous studies, there has been significant thinning in the area around the hippocampus and parts of it are being left out in the mask, such as the para-hippocampal region.
Regards
Joshua
On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
The residual FWHM is measured from the data itself. You apply a certain amount of smoothing, but there is already some smoothness to the data, so the final fwhm is a combination of what is already there and what you apply. A fwhm of 47 is huge and may indicate that something is wrong. What is the input? cortical thickness? Are you using your own mask or is this a whole hemisphere analysis?
doug
On 6/2/13 10:29 PM, Joshua deSouza wrote:
Hello Doug,
Thank you for your quick replies to my queries. Really appreciate it.
I have found the files containing the cortical thickness values. Thank you. I assume that the order in which they follow are based on the fsgd file and the cluster annotation numbers.
I was just slightly confused about the residual fwhm. I have already done a smoothing of 15 on the file and have recieved a residual value of 47, which I assume is extremely large. Since I'm finding out values for the entire cortex I cannot do a glmfit-sim as there are no fwhm cache values of 47. Could you please tell me what the residual values mean? What do you recommend I do? Is there anything I can read up on to find out more about this? (Please pardon my questions if they seem a little trivial)
Thank you
Joshua
On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
This file is always created by mri_glmfit-sim. It might be named something different depending on your parameters (should always end in y.ocn.dat) doug
On 6/2/13 3:57 AM, Joshua deSouza wrote:
Hi Doug,
This file that your saying, will be created after glmfit-sim is done using the cache function and a threshold of 1.3 and absolute ,with y being the fsgd file? Am I understanding this correctly?
Thank you
Joshua
On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
There should be a file called something like cache.th13.abs.y.ocn.dat. This will have a column for each cluster and a row for each subject. The value in the row will be the input for each subject. doug
On 05/30/2013 11:21 PM, Joshua deSouza wrote:
Hello everyone,
Please pardon my rather simple question
I have done a GLM fit anlysis and have obtained a file sig.mgh alonf with a few others after the analysis.As I know, I do not have to create ROIs in order to do this. I also understand that doing a multiple comparison analysis just compares the regions of importance and evaluates them giving the most resilient cluster depending on the threshold. So, this does not give a thickness estimate. I would like to know how do I get the cortical thickness values from the results? If so, can I do it after glmfit?
And thanks Doug for your help in the other questions that I had prior to this!
Thank you
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: 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/
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 Joshua, when you add --fwhm 15 to the command line you are instructing mri_glmfit to smooth by 15mm. Is this what you want? Or is the data already smoothed? doug
On 6/3/13 12:26 AM, Joshua deSouza wrote:
Hi Doug,
The command line is mri_glmfit --y lh.t.15.mgh --fsgd t.txt dods --C t1.txt --surface fsaverage lh --cortex --fwhm 15 --glmdir lh.t.15.glmdir
I am doing a whole hemisphere analysis and am measuring cortical thickness. I do not have my own mask but I have doubts about the mask that has been produced because from previous studies, there has been significant thinning in the area around the hippocampus and parts of it are being left out in the mask, such as the para-hippocampal region.
Regards
Joshua
On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The residual FWHM is measured from the data itself. You apply a certain amount of smoothing, but there is already some smoothness to the data, so the final fwhm is a combination of what is already there and what you apply. A fwhm of 47 is huge and may indicate that something is wrong. What is the input? cortical thickness? Are you using your own mask or is this a whole hemisphere analysis? doug On 6/2/13 10:29 PM, Joshua deSouza wrote:Hello Doug, Thank you for your quick replies to my queries. Really appreciate it. I have found the files containing the cortical thickness values. Thank you. I assume that the order in which they follow are based on the fsgd file and the cluster annotation numbers. I was just slightly confused about the residual fwhm. I have already done a smoothing of 15 on the file and have recieved a residual value of 47, which I assume is extremely large. Since I'm finding out values for the entire cortex I cannot do a glmfit-sim as there are no fwhm cache values of 47. Could you please tell me what the residual values mean? What do you recommend I do? Is there anything I can read up on to find out more about this? (Please pardon my questions if they seem a little trivial) Thank you Joshua On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: This file is always created by mri_glmfit-sim. It might be named something different depending on your parameters (should always end in y.ocn.dat) doug On 6/2/13 3:57 AM, Joshua deSouza wrote:Hi Doug, This file that your saying, will be created after glmfit-sim is done using the cache function and a threshold of 1.3 and absolute ,with y being the fsgd file? Am I understanding this correctly? Thank you Joshua On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: There should be a file called something like cache.th13.abs.y.ocn.dat. This will have a column for each cluster and a row for each subject. The value in the row will be the input for each subject. doug On 05/30/2013 11:21 PM, Joshua deSouza wrote: > Hello everyone, > > Please pardon my rather simple question > > I have done a GLM fit anlysis and have obtained a file sig.mgh alonf > with a few others after the analysis.As I know, I do not have to > create ROIs in order to do this. I also understand that doing a > multiple comparison analysis just compares the regions of importance > and evaluates them giving the most resilient cluster depending on the > threshold. So, this does not give a thickness estimate. I would like > to know how do I get the cortical thickness values from the results? > If so, can I do it after glmfit? > > And thanks Doug for your help in the other questions that I had prior > to this! > > Thank you > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
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Douglas Greve -
Douglas N Greve
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Joshua deSouza