Hi FS experts, I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with --bg option). I have 4 contrasts, but only the first one has some files of corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the log file in the attachment. However, previously I ran mri_glmfit by DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected results. Thanks. All the best. Rujing Zha
2014-02-21
charujing123
When you actually run the simulation, it only runs it for the first contrast. The simulation is the same for all contrasts, so you can just copy the csd files from the first contrast to the others, then run mri_glmfit-sim with the --no-sim option doug
On 2/21/14 5:47 AM, charujing123 wrote:
Hi FS experts, I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with --bg option). I have 4 contrasts, but only the first one has some files of corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the log file in the attachment. However, previously I ran mri_glmfit by DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected results. Thanks. All the best. Rujing Zha 2014-02-21
charujing123
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi doug and others, Thanks doug. According this information https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ViewCSDFi..., I try to find the csd files in the csd folder(I am not sure this is what you just told me). But there are the csd files as I run simulation with --bg option. Also I try to find the csd files in the first contrast directory, but I think, maybe I am wrong, none of these is csd files that you suggest. Doug, would you please describe it more detailly, as I am a new user for FS? Thanks doug and others. All the best. Rujing Zha
2014-02-22
charujing123
发件人：Douglas Greve greve@nmr.mgh.harvard.edu 发送时间：2014-02-21 23:49 主题：Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
When you actually run the simulation, it only runs it for the first contrast. The simulation is the same for all contrasts, so you can just copy the csd files from the first contrast to the others, then run mri_glmfit-sim with the --no-sim option doug
On 2/21/14 5:47 AM, charujing123 wrote:
Hi FS experts, I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with --bg option). I have 4 contrasts, but only the first one has some files of corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the log file in the attachment. However, previously I ran mri_glmfit by DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected results. Thanks. All the best. Rujing Zha
2014-02-21
charujing123
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sorry, you are right, the csd files are in the csd folder. The csf file will have a name with the contrast name in it. Copy it to a file with a name where you substitute the old contrast name for another contrast name. doug
On 02/21/2014 09:18 PM, charujing123 wrote:
Hi doug and others, Thanks doug. According this information https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ViewCSDFi..., I try to find the csd files in the csd folder(I am not sure this is what you just told me). But there are the csd files as I run simulation with --bg option. Also I try to find the csd files in the first contrast directory, but I think, maybe I am wrong, none of these is csd files that you suggest. Doug, would you please describe it more detailly, as I am a new user for FS? Thanks doug and others. All the best. Rujing Zha 2014-02-22
charujing123
*发件人：*Douglas Greve greve@nmr.mgh.harvard.edu *发送时间：*2014-02-21 23:49 *主题：*Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss *收件人：*"freesurfer"freesurfer@nmr.mgh.harvard.edu *抄送：*
When you actually run the simulation, it only runs it for the first contrast. The simulation is the same for all contrasts, so you can just copy the csd files from the first contrast to the others, then run mri_glmfit-sim with the --no-sim option doug
On 2/21/14 5:47 AM, charujing123 wrote:
Hi FS experts, I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with --bg option). I have 4 contrasts, but only the first one has some files of corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the log file in the attachment. However, previously I ran mri_glmfit by DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected results. Thanks. All the best. Rujing Zha 2014-02-21
charujing123
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@nmr.mgh.harvard.edu
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charujing123 -
Douglas Greve -
Douglas N Greve