Hi, I just ran the mri_glmfit-sim command on our data and there were a couple of things I did not understand. We had previously ran the same command on fewer subjects and it had taken about 10 days to run. This time around it only took 2 days even though we had more subjects (there don't seem to be any errors; it just finished sooner). Another thing I noticed was that previously the command wrote several folders (ones that measured thickness, sulc, area, etc. both average and difference between the subject groups) into the output folder we specified in the "glmdir" option. This time it only wrote one (just the average thickness).
As far as I can tell, I followed the command exactly as before (copied and pasted the command) with the same number of interations. I also followed the Group Analysis tutorial from the wiki.
Can anybody shed some light on this? Why this discrepancy between the two?
Thank you, Devdutta
What are your command lines? In general, it's a good idea to send this each time, even if you're not sure it's useful.
doug
Devdutta W wrote:
Hi, I just ran the mri_glmfit-sim command on our data and there were a couple of things I did not understand. We had previously ran the same command on fewer subjects and it had taken about 10 days to run. This time around it only took 2 days even though we had more subjects (there don't seem to be any errors; it just finished sooner). Another thing I noticed was that previously the command wrote several folders (ones that measured thickness, sulc, area, etc. both average and difference between the subject groups) into the output folder we specified in the "glmdir" option. This time it only wrote one (just the average thickness).
As far as I can tell, I followed the command exactly as before (copied and pasted the command) with the same number of interations. I also followed the Group Analysis tutorial from the wiki.
Can anybody shed some light on this? Why this discrepancy between the two?
Thank you, Devdutta
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Here is the command line I am using. the same one was used both times; only the glmdir was different.
mri_glmfit-sim \ --glmdir /data/zonda1/freesurfer_subjects/qdec/rh.area \ --sim mc-z 5000 2 mc-z.abs.2 \ --sim-sign abs \ --overwrite
On Wed, Jul 22, 2009 at 12:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
What are your command lines? In general, it's a good idea to send this each time, even if you're not sure it's useful.
doug
Devdutta W wrote:
Hi, I just ran the mri_glmfit-sim command on our data and there were a couple of things I did not understand. We had previously ran the same command on fewer subjects and it had taken about 10 days to run. This time around it only took 2 days even though we had more subjects (there don't seem to be any errors; it just finished sooner). Another thing I noticed was that previously the command wrote several folders (ones that measured thickness, sulc, area, etc. both average and difference between the subject groups) into the output folder we specified in the "glmdir" option. This time it only wrote one (just the average thickness).
As far as I can tell, I followed the command exactly as before (copied and pasted the command) with the same number of interations. I also followed the Group Analysis tutorial from the wiki. Can anybody shed some light on this? Why this discrepancy between the two?
Thank you, Devdutta
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
MC-Z will be independent of the number subjects. The z simulation assumes an infinite DOF.
doug
Devdutta W wrote:
Here is the command line I am using. the same one was used both times; only the glmdir was different.
mri_glmfit-sim \ --glmdir /data/zonda1/freesurfer_subjects/qdec/rh.area \ --sim mc-z 5000 2 mc-z.abs.2 \ --sim-sign abs \ --overwrite
On Wed, Jul 22, 2009 at 12:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What are your command lines? In general, it's a good idea to send this each time, even if you're not sure it's useful. doug Devdutta W wrote: Hi, I just ran the mri_glmfit-sim command on our data and there were a couple of things I did not understand. We had previously ran the same command on fewer subjects and it had taken about 10 days to run. This time around it only took 2 days even though we had more subjects (there don't seem to be any errors; it just finished sooner). Another thing I noticed was that previously the command wrote several folders (ones that measured thickness, sulc, area, etc. both average and difference between the subject groups) into the output folder we specified in the "glmdir" option. This time it only wrote one (just the average thickness). As far as I can tell, I followed the command exactly as before (copied and pasted the command) with the same number of interations. I also followed the Group Analysis tutorial from the wiki. Can anybody shed some light on this? Why this discrepancy between the two? Thank you, Devdutta ------------------------------------------------------------------------ _______________________________________________ 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 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
freesurfer@nmr.mgh.harvard.edu
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Devdutta W -
Douglas N Greve