You can add something like --mul 1000 to the mri_segstats command line to multiply the values by 1000 to get 3 more decimal places doug
On 02/12/2015 02:06 AM, Thomas Potrusil wrote: > Hi Anastasia, > you´re right, the values are reasonable! The problem is that I cannot > read out all the decimal places that I can see in FreeView as > described! When I save the values of distinct ROIs to a .stats file, I > can only see e.g. 0.0007 but I need 0.000770333 for further > processing. Do you have any suggestions how I can get more decimal > places on a .stats file? > Thanks a lot, Tom > *Gesendet:* Mittwoch, 11. Februar 2015 um 17:39 Uhr > *Von:* "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > *An:* "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > *Betreff:* Re: [Freesurfer] DTI question > Hi Tom - These are reasonable values for mean diffusivity (a.k.a. > ADC). Only FA is normalized to take values in the 0-1 range. a.y On > Wed, 11 Feb 2015, Thomas Potrusil wrote: > Dear FreeSurfers! > A > question concerning DTI analysis came up: > > I already run dt_recon > on my dataset which works very well. I also used the output to extract > FA-values of distinct ROIs - no Problem. Now I want to do the same for > ADC but I only get > values in my .stats files like 0.0007 or 0.0008. > > I use the following code: > > dt_recon --i $dcmfile --b bvals > bvecs --s $subj --o $outdir_dt_recon > > mri_vol2vol --mov > $outdir_dt_recon/adc.nii \ --reg $outdir_dt_recon/register.dat \ > --fstarg --interp nearest \ --o $outdir_dt_recon/adc.anat.mgh > > > mri_segstats \ --seg $SUBJECTS_DIR/$subj/mri/wmparc.mgz \ --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt \ --id 12 --id 51 --id 2 > --id 41 --id 16 --id 13 --id 52 --id 27 --id 59\ > --i > $outdir_dt_recon/adc.anat.mgh --seg-erode 1 --sum > $outdir_dt_recon/adc.stats > > When I load adc.anat.mgh into > FreeView and scroll to a ROI, I can see a value like 0.000770333! This > means (for me) that the value is 'there' but has to be multiplied by > 10^3?! Do you > have any suggestions how I can get these values to a > .stats file? > > Thanks a lot, > Tom > > >_______________________________________________ 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 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
