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>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 > <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 <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. 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 >>>> >>>> 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. >>>>> >>>>> >>>> >>>> >>> >>> >> >> >
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