why did you not use fscalc, eg, fscalc var.mgh -sqrt -o stderr.mgh
On 12/21/2015 03:04 PM, John Anderson wrote: > Thanks Doug, > I used the command "mris_calc gammavar.mgh sqrt" and the output was: > _"Saving result to 'out.mgz' (type = MGH _)" > *Then* I ran the command "mris_calc out.mgz stats" and the output was : > Size [ 163842 ] > Min@(index) [ 0.000000 (161385) ] > Max@(index) [ 0.259395 (18208) ] > Mean [ 0.097956 ] > Std [ 0.040943 ] > Sum [ 16049.365234 ] > Prod [ 0.000000 ] > In order to calculate the standard error is it fine if I use > _*mris_calc *__*gammavar.mgh stats*_ the I divide the *Std* of > gammavar.mgh by the square root of the sample size ( number of > subjects included in the analysis)? > Thanks a lot! > *Sent:* Monday, December 21, 2015 at 2:44 PM > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Qdec visualization > it helps to see the error msg, but my guess is that you need to specify > an mgh file, not a txt file. This will give you the voxel-wise stderr, > not a standard error for the cluster (which does not make sense) > > On 12/21/2015 02:38 PM, John Anderson wrote: > > Hi Doug, > > Given that the standard variance can be calculated using the command > > "mris_calc" and the flag "-sqrt" what is the correct command to do > > this calculation? > > I tried: > > mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly > > what I am doing wrong? > > Bests, > > John > > *Sent:* Monday, December 21, 2015 at 2:20 PM > > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > > *To:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] Qdec visualization > > QDEC cannot but the information may be in the output folder. There > > should be a file called gammavar.mgh. This will be the standard variance > > (so take the square root) > > > > On 12/21/2015 02:08 PM, John Anderson wrote: > > > Thanks you very much Doug, > > > Please one more question. Is there any way in Qdec to get the stamdard > > > error (SE) ? > > > Bests, > > > John > > > *Sent:* Monday, December 21, 2015 at 11:43 AM > > > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > > > *To:* freesurfer@nmr.mgh.harvard.edu > > > *Subject:* Re: [Freesurfer] Qdec visualization > > > The correction for multiple comparisons is cluster-based. Each cluster > > > gets a single number. In the display, all the vertices get that same > > > number. > > > > > > On 12/18/2015 03:17 PM, John Anderson wrote: > > > > Hi Freesurfer experts, > > > > I am using Qdec in Freesurfer 5.3 to do some cortical thickness > > > > comparisons between two groups. > > > > > > > > Before corrcting the results for multiple comparisons ( monte carlo > > > > simulation) the significant differnce between the groups is > visualized > > > > as a range of color while after correcting for multiple copmparisons > > > > the color of the statistical map is usinform ( Attached) > > > > Is ther any way to visualze the results as a range of color after > > > > correcting the results for multiple comparsiosn > > > > > > > > Thanks in advance for any advice > > > > Bests, > > > > John Anderson > > > > > > > > Senior Research Associate > > > > Psychological and Brain Sciences Dept. > > > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH > 03755 > > > > Phone: +1 (603) 646-9834 > > > > Fax: +1 (603) 646-1419 > > > > > > > > > > > > _______________________________________________ > > > > 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 > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://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. > > > > > > > > > _______________________________________________ > > > 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 > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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 > > > > > > _______________________________________________ > > 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 > <http://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 > > > _______________________________________________ > 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
