Hi Doug,
Thanks for helping me 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?
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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Hi Doug,
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 \
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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Hi Doug,
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 \
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Hi Doug,
freesurfer@nmr.mgh.harvard.edu
-
Antonella Kis -
Douglas N Greve