under the "Mean" column On 11/06/2015 07:46 AM, std...@virgilio.it wrote: > I have run > mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig.masked. > nii.gz rh parc --i subj/fc.seed.surf.rh/R_seed/z.nii.gz --sum > summaryfile > > and I have obtained 9 columns and 5 rows. > I'm confused on results. Where is the mean z-score for cache.th13.neg. > sig.masked.nii.gz? > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev > Min Max Range > 1 -4 7 7.0 Seg-004 -2.4544 0.5023 > -3.2164 -1.7619 1.4545 > 2 -3 153 153.0 Seg-003 -2.6662 1.4724 > -6.2120 1.7587 7.9707 > 3 -2 848 848.0 Seg-002 -2.4930 2.0088 > -6.4504 2.3528 8.8032 > 4 -1 1518 1518.0 Seg-001 -2.1416 1.6727 > -6.4227 2.5420 8.9648 > 5 0 161316 161316.0 Seg0000 1.4152 1.6218 > -7.0471 14.1452 21.1923 > > Because my data are on surface mri_surfcluster should be helpful? > > Thanks. > > > Stefano > > >> ----Messaggio originale---- >> Da: gr...@nmr.mgh.harvard.edu >> Data: 3-nov-2015 19.55 >> A: <freesurfer@nmr.mgh.harvard.edu> >> Ogg: Re: [Freesurfer] R: Re: average z-score of each subject from a > common cluster >> look in the summaryfile. Also, don't use --seg z.nii.gz. In the > command >> below, it works because you have --annot afterwards, but in general > it >> is not correct >> >> On 10/30/2015 04:22 PM, std...@virgilio.it wrote: >>> Thanks. >>> I have obtained: >>> >>> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ >>> >>> cwd >>> >>> cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh aparc -- > i >>> z.nii.gz --sum summaryfile >>> >>> sysname Darwin >>> >>> hostname iMac-di-Stefano.local >>> >>> machine x86_64 >>> >>> user Stefano >>> >>> UseRobust 0 >>> >>> Loading z.nii.gz >>> >>> Loading z.nii.gz >>> >>> Voxel Volume is 1 mm^3 >>> >>> Generating list of segmentation ids >>> >>> Found 22 segmentations >>> >>> Computing statistics for each segmentation >>> >>> 0 -7 2 2.000 >>> >>> 1 -6 110 110.000 >>> >>> 2 -5 255 255.000 >>> >>> 3 -4 518 518.000 >>> >>> 4 -3 1190 1190.000 >>> >>> 5 -2 1692 1692.000 >>> >>> 6 -1 4104 4104.000 >>> >>> 7 0 61577 61577.000 >>> >>> 8 1 42598 42598.000 >>> >>> 9 2 28146 28146.000 >>> >>> 10 3 14859 14859.000 >>> >>> 11 4 5845 5845.000 >>> >>> 12 5 1899 1899.000 >>> >>> 13 6 485 485.000 >>> >>> 14 7 116 116.000 >>> >>> 15 8 75 75.000 >>> >>> 16 9 74 74.000 >>> >>> 17 10 78 78.000 >>> >>> 18 11 65 65.000 >>> >>> 19 12 104 104.000 >>> >>> 20 13 45 45.000 >>> >>> 21 14 5 5.000 >>> >>> >>> How I can know the meaning of this number? Where is z? >>> >>> I have tried also with: >>> >>> mri_segstats --seg z.nii.gz --annot Control_21 rh aparc --i z.nii. > gz >>> --sum summaryfile --mask >>> .../fc.ramgseed.surf.rh/R_Amygdala/my-glm.wls/group.diff/cache.th13. > neg.sig.masked.nii.gz >>> --avgwfvol mrivol >>> >>> >>> but I have problem with interpretation. >>> >>> >>> >>> Stefano >>> >>> >>> ----Messaggio originale---- >>> Da: gr...@nmr.mgh.harvard.edu >>> Data: 30-ott-2015 16.17 >>> A: <freesurfer@nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] average z-score of each subject from a >>> common cluster >>> >>> >>> >>> On 10/30/15 7:16 AM, std...@virgilio.it wrote: >>>> Hi list, >>>> I have two queries, please. >>>> >>>> I'd like to have the z-score from my rsfMRI data (seed- > analyis). >>>> 1) I have extract the z-score from the Vtx Max >>>> >>>> In details, after groups comparison analysis, I have opened >>>> the cache.th13.pos.sig.cluster.summary contained in group.diff >>>> folder and I have read the Vtx Max coordinates. >>>> Next, I have open the z.nii.gz of each subject and I have >>>> expected the z-score from the vertex which have the Vtx Max >>>> coordinates. >>>> >>>> Is this procedure corrected? >>> Yes >>>> 2) z-score of each subject from a common cluster >>>> >>>> I would like to use the cluster which shows the group > difference >>>> (cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I would >>>> extract from it the average of the z-score which is contained > in >>>> each subject. >>>> How should I do? >>> Use mri_segstats passing the z map as the input (--i) and the >>> cluster map as the seg. The output will be --sum. Run with -- > help >>> for more info >>>> Thanks. >>>> >>>> >>>> Stefano >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> >> >> 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
