Re: [Freesurfer] Editing masks
Hello Bruce, Yes, I am using the surfaces for this. I am trying to find cortical thickness differences between populations. I do not think that the mask covers the entire hippocampal area, just leaving out the corpus callosum. How would I include these areas into the mask? Thank you, Joshua On Tue, Jun 11, 2013 at 8:29 PM, Bruce Fischl wrote: > Hi Joshua > > are you using the surfaces for this? If so, you shouldn't as they are > undefined in those regions (since they have internal laminar structure that > is different than what we expect). What are you trying to achieve? > > cheers > Bruce > > On Tue, 11 Jun 2013, Joshua deSouza wrote: > > Hello all, >> >> I am having a problem with generating values of the vertices at the >> hippocampal area. I believe it is a masking issue as reviewing the mask >> after the glmfit analysis I see that the mask does not cover the entire >> medial region excluding the corpus callosum. Can I do anything to change >> the >> mask as to add deeper brain regions at the hippocampal area? >> >> Thank you >> >> Joshua >> >> >> > > 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<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 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] Editing masks
Hello all, I am having a problem with generating values of the vertices at the hippocampal area. I believe it is a masking issue as reviewing the mask after the glmfit analysis I see that the mask does not cover the entire medial region excluding the corpus callosum. Can I do anything to change the mask as to add deeper brain regions at the hippocampal area? Thank you Joshua ___ 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] Cortical thickness
Hello Doug, Thanks for your help on this. Ive run it again and there doesnt seem to be a problem. Its just that when I smooth it by 15 now the residual is about 23. When I ran it the other time, the residual was 47 for some unknown reason. Regards, Joshua On Thu, Jun 6, 2013 at 10:14 PM, Douglas N Greve wrote: > > I think when you smooth it that much strange things happen. Try just one > smoothing of 15mm. > > > > > On 06/06/2013 03:36 AM, Joshua deSouza wrote: > >> Hi Doug, >> >> I did not specify anything in the mris_preproc, so it would be using the >> unsmoothed data. I only specify smoothing during the mri_surf2surf, which >> is 15 and then run glmfit. So what could be the reasons why i'm getting a >> residual fwhm of 47? >> >> Regards, >> >> Joshua >> >> On Thu, Jun 6, 2013 at 12:16 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu>> >> wrote: >> >> Unless you specify otherwise, mris_preproc will use unsmoothed >> data. If you then smooth it with mri_surf2surf and run run >> mri_glmfit with --fwhm then you will be smoothing it twice. >> doug >> >> >> >> >> On 06/04/2013 09:49 PM, Joshua deSouza wrote: >> >> Hello Doug, >> >> Each individuals subject data has already been smoothed by 5 >> 10 15 20 and 25 through the qache function during the initial >> processing. >> >> I'm a little confused now. I thought that the mri_preproc >> would use the non-smoothed values of the subjects and create >> an mgh file. After which I smooth the mgh file and then use >> mri_glmfit to analyse it according to the contrasts. >> >> If the above is not the case and the subject data has already >> been smoothed, then what should I do if I wish my final mgh >> file to have a smoothing value of 15 before doing a glmfit on it? >> >> Thank you, >> >> Joshua >> >> >> On Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza >> > <mailto:desouzajoshua00@gmail.**com >> > >> <mailto:desouzajoshua00@gmail.**com >> >> <mailto:desouzajoshua00@gmail.**com >>> >> wrote: >> >> Hello Doug, >> >> Each individuals subject data has already been smoothed by >> 5 10 15 >> 20 and 25 through the qache function during the initial >> processing. >> >> I'm a little confused now. I thought that the mri_preproc >> would >> use the non-smoothed values of the subjects and create an mgh >> file. After which I smooth the mgh file and then use >> mri_glmfit to >> analyse it according to the contrasts. >> >> If the above is not the case and the subject data has >> already been >> smoothed, then what should I do if I wish my final mgh file to >> have a smoothing value of 15 before doing a glmfit on it? >> >> Thank you, >> >> Joshua >> >> On Mon, Jun 3, 2013 at 11:13 PM, Douglas Greve >> > <mailto:gr...@nmr.mgh.harvard.**edu > >> <mailto:gr...@nmr.mgh.harvard.**edu >> >> <mailto:gr...@nmr.mgh.harvard.**edu >>> >> wrote: >> >> >> 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 >> thinn
Re: [Freesurfer] Cortical thickness
Hi Doug, I did not specify anything in the mris_preproc, so it would be using the unsmoothed data. I only specify smoothing during the mri_surf2surf, which is 15 and then run glmfit. So what could be the reasons why i'm getting a residual fwhm of 47? Regards, Joshua On Thu, Jun 6, 2013 at 12:16 AM, Douglas N Greve wrote: > Unless you specify otherwise, mris_preproc will use unsmoothed data. If > you then smooth it with mri_surf2surf and run run mri_glmfit with --fwhm > then you will be smoothing it twice. > doug > > > > > On 06/04/2013 09:49 PM, Joshua deSouza wrote: > >> Hello Doug, >> >> Each individuals subject data has already been smoothed by 5 10 15 20 and >> 25 through the qache function during the initial processing. >> >> I'm a little confused now. I thought that the mri_preproc would use the >> non-smoothed values of the subjects and create an mgh file. After which I >> smooth the mgh file and then use mri_glmfit to analyse it according to the >> contrasts. >> >> If the above is not the case and the subject data has already been >> smoothed, then what should I do if I wish my final mgh file to have a >> smoothing value of 15 before doing a glmfit on it? >> >> Thank you, >> >> Joshua >> >> >> On Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza < >> desouzajoshu...@gmail.com >> <mailto:desouzajoshua00@gmail.**com>> >> wrote: >> >> Hello Doug, >> >> Each individuals subject data has already been smoothed by 5 10 15 >> 20 and 25 through the qache function during the initial processing. >> >> I'm a little confused now. I thought that the mri_preproc would >> use the non-smoothed values of the subjects and create an mgh >> file. After which I smooth the mgh file and then use mri_glmfit to >> analyse it according to the contrasts. >> >> If the above is not the case and the subject data has already been >> smoothed, then what should I do if I wish my final mgh file to >> have a smoothing value of 15 before doing a glmfit on it? >> >> Thank you, >> >> Joshua >> >> On Mon, Jun 3, 2013 at 11:13 PM, Douglas Greve >> > <mailto:gr...@nmr.mgh.harvard.**edu>> >> wrote: >> >> >> 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 >>> >> <mailto:gr...@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.
Re: [Freesurfer] Cortical thickness
Hello Doug, Each individuals subject data has already been smoothed by 5 10 15 20 and 25 through the qache function during the initial processing. I'm a little confused now. I thought that the mri_preproc would use the non-smoothed values of the subjects and create an mgh file. After which I smooth the mgh file and then use mri_glmfit to analyse it according to the contrasts. If the above is not the case and the subject data has already been smoothed, then what should I do if I wish my final mgh file to have a smoothing value of 15 before doing a glmfit on it? Thank you, Joshua On Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza wrote: > Hello Doug, > > Each individuals subject data has already been smoothed by 5 10 15 20 and > 25 through the qache function during the initial processing. > > I'm a little confused now. I thought that the mri_preproc would use the > non-smoothed values of the subjects and create an mgh file. After which I > smooth the mgh file and then use mri_glmfit to analyse it according to the > contrasts. > > If the above is not the case and the subject data has already been > smoothed, then what should I do if I wish my final mgh file to have a > smoothing value of 15 before doing a glmfit on it? > > Thank you, > > Joshua > > On Mon, Jun 3, 2013 at 11:13 PM, Douglas Greve > wrote: > >> >> 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 > > 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 < >>> gr...@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 >>>> >>>> Jos
Re: [Freesurfer] Cortical thickness
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 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 > 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 < >> gr...@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 >>> gr...@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 >>> http
Re: [Freesurfer] Cortical thickness
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 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 < > gr...@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 >> gr...@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. >> >> > > ___ 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] Cortical thickness
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 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 > gr...@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. > > ___ 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] Cortical thickness
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 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] mri_glmfit files
Hello all, I would just like to know what is the significance of the files that are produced after a glmfit is done. I was trying to find a write up online but I was not able to. They include : - cnr.mgh - F.mgh - gamma.mgh - gammavar.mgh - sig.mgh 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] Issues with Cluster generation
Hello all, I am facing a problem whereby after running GLMfit and cluserwise correction for multiple comparisons using the monte-carlo method, I was unable to generate any clusters. I do have significant images produced for the glmfit. All procedures were done according to the tutorial to match the effects under FSGD. There are no clusters available even when I set the cwpvalthresh to .999 which is supposed to show all clusters. What is the cluster generation dependent upon? As my glmfit does show significant areas. Please advise ___ 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] Fwd: Error with experimental design using FSGD
Hello Sir/Madam, I am currently running a statistical test using the FSGD method. I am encountering a problem in relation to the creation of the glmdir folder when I run the mri_glmfit function. I recieve an ERROR message that tells me that the design matrix (automatically generated) is ill conditioned or badly scaled, condo = 10565.7. All the steps before creating the glmdir folder have been done in accordance with the FSGD group analysis tutorial on the freesurfer wiki. The command line is : mri_glmfit --y lh.thomas4.10.mgh --fsgd thomas4.txt dods --C t4.txt --surf fsaverage lh --cortex --glmdir lh.thomas4.glmdir The FSGD file = thomas4.txt ( contains 2 groups and 5 variables) The data matrix = Xg.dat The contrast matrix = t4.txt There are 3 columns of variables that have discreet values of either 1 or 2. However I have tried this with another FSGD file (thomas3.txt) that contained 4 variables of which 2 were continous and the other 2 were in 1s' and 2s'. The contrast matrix of thomas3.txt = C.dat The design matrix of thomas3.txt = Xg1.dat I was able to generate a glmdir using mri_glmfit with thomas3.txt and generate a surface for tksurfer to use. The file created was the sig.mgh file which was then compared with the fsaverage files. However once I added another variable titled "voxel" in thomas4.txt, I received the error message. I did a correlation of the columns containing 1s and 2s in the FSGD file thomas4.txt using Matlab and have not found any significant correlation with each other. Please do advise on how to solve this issue and also from where the problem could stem from as I am unsure as to the nature of the problem. Thank You for your patience and assistance Joshua GroupDescriptorFile 1 Title thomas4 Class group0bp Class group0n Variables gender Age TIV handedness voxel Input 003_S_1059 group0n 2 84.60 1.471 2 Input 006_S_0547 group0n 1 75.94 1.581 2 Input 027_S_0404 group0n 2 87.92 1.271 2 Input 057_S_1379 group0n 1 87.93 1.721 1 Input 062_S_0690 group0n 1 79.70 1.581 1 Input 116_S_1083 group0n 2 72.04 1.382 2 Input 130_S_1337 group0n 1 71.53 1.582 2 Input 136_S_0299 group0n 2 89.17 1.471 2 Input 137_S_0796 group0n 1 80.47 1.731 2 Input 002_S_0619 group0bp1 77.51 1.951 2 Input 005_S_0221 group0bp1 67.60 1.711 2 Input 005_S_1341 group0bp2 71.72 1.251 2 Input 007_S_0316 group0bp1 80.94 1.521 2 Input 007_S_1304 group0bp2 74.88 1.271 2 Input 009_S_1354 group0bp2 58.93 1.231 2 Input 011_S_0003 group0bp1 81.33 1.8 1 1 Input 011_S_0010 group0bp2 73.91 1.411 1 Input 012_S_0720 group0bp2 77.52 1.331 2 Input 012_S_0803 group0bp2 84.80 1.371 2 Input 021_S_0753 group0bp1 65.65 1.621 2 Input 021_S_1109 group0bp2 77.90 1.351 2 Input 022_S_0129 group0bp2 80.25 1.361 1 Input 022_S_0219 group0bp1 74.55 1.341 1 Input 023_S_0093 group0bp2 77.36 1.341 1 Input 027_S_0850 group0bp1 78.23 1.481 2 Input 027_S_1081 group0bp1 84.67 1.6 1 2 Input 027_S_1082 group0bp2 69.58 1.381 2 Input 032_S_0147 group0bp2 59.82 1.6 1 2 Input 033_S_1281 group0bp2 77.72 1.391 2 Input 033_S_1285 group0bp2 80.13 1.571 2 Input 036_S_0577 group0bp2 72.49 1.371 1 Input 037_S_0627 group0bp2 58.67 1.361 2 Input 053_S_1044 group0bp1 65.75 1.591 2 Input 062_S_0535 group0bp1 76.83 1.691 1 Input 067_S_1185 group0bp1 62.09 1.522 1 Input 082_S_1079 group0bp1 78.14 1.761 2 Input 098_S_0149 group0bp1 87.82 1.571 2 Input 099_S_0470 group0bp2 86.77 1.461 1 Input 099_S_0492 group0bp1 87.46 1.561 2 Input 114_S_0374 group0bp2 76.03 1.4 1 1 Input 123_S_0094 group0bp2 70.82 1.5 1 2 Input 128_S_0266 group0bp1 85.59 1.781 2 Input 131_S_0691 group0bp1 64.48 1.732
