----- Forwarded Message ----- From: Antonella Kis atorok9@yahoo.com To: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Friday, September 30, 2011 12:31 PM Subject: Re: [Freesurfer] Default for fwhm while running mri_glmfit
I see.I am not sure what exactly you mean by an outlier in my data,but if there will be an outlier, why the mri_glmfit --sim is working for a smoothing level 15?
Also what means in your last sentence "when the smoothing level is only 20"? Isn't 20 the max smoothing level? And while smoothing level increases shouldn't fwhm increase?
How different will be my results from the real one if I change the fwhm value from 31.843147 in the mri_glmfit.log file to a value of 30 and the run mri_glmfit-sim? I tried this and I am not getting the error any more but there are more clusters coming up and I have a different size for original clusters so I suppose the cortical thickness values cached in the tables are not good. Can I do this trick?
Many thanks, AK
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 30, 2011 11:40 AM Subject: Re: [Freesurfer] Default for fwhm while running mri_glmfit
There is no one smoothing level that is right. In general, people tend to just go with a default value. I think that 20 is pretty high, I usually go with 5-15. You might examine your data to see if you have an outlier. I think it is unusual for you to get an output fwhm of over 30 when the smoothing level is only 20. doug
Antonella Kis wrote:
Hi Doug,
Thanks for helping again. I used smoothing level of 20 because I was told to use this smoothing. If I use the 15 I am not getting the error but I need to use the 20.Is there a way that I can make it work/correct this error and get my tables cached in this case?
Is fwhm= 15 the default in FS while running the mri_gmlfit (mri_surfcluster? What if my data was smoothed at 10 while running the mris_preproc --cache-in thickness.fwhm20.fsaverage
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Please advise. Thank you. AK
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Antonella Kis atorok9@yahoo.com *Cc:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu; "fischl@nmr.mgh.harvard.edu" fischl@nmr.mgh.harvard.edu *Sent:* Friday, September 30, 2011 10:52 AM *Subject:* Re: Error due to fwhm
That exceeds the valued for which the tables are cached. What smoothing level did you use? doug
Antonella Kis wrote:
Hi,
When I ran the QDEC on patients with abnormal side right, the fwhm
for the clusters at thresh 2 is fwhm = 31.843147.
Then, I ran mri_glmfit-sim on the QDEC output and it gives me the
following error (cannot find fwhm 32):
ERROR: cannot find
/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm32/neg/th20/mc-z.csd
Is there a way that I can change the fhwm while running
mri_glmfit-sim from 32 to 31.843147 or how I can correct this error?
Many thanks. AK
-- 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
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Hi Doug,