When you run mri_surfcluster, save an output cluster number (--ocn) output, then feed that into mri_segstats.
On 7/18/19 11:44 AM, Mark Wagshul wrote: > > External Email - Use Caution > > Hi. I have a question about cluster size determination within Freesurfer. > > We are running linear mixed model on our Freesurfer generated volume > data over the left and right cortex parcellations, and would like to > look at cluster size at the p < 0.01 cluster-forming threshold level. > > 1)After running the models, we have created a .mgh image of the > F-stats results, separately for the negative and positive results, > saving them with fs_write_Y. > > 2)We then run these data through mri_surfcluster, which reports the > maximum cluster size of 216 voxels. This was run with the command: > > a.mri_surfcluster --hemi lh --in F_lhstats.mgh --o F_lhstats > _negCluster.mgh --subject fsaverage --thmin 6.8 --sign pos > > b.The “sign” is set to positive because this is running on F-numbers. > > 3)Next, we run mri_segstats on the output of the last command to get > the location and sizes of the individual clusters, as follows: > > a.mri_segstats --seg F_lhstats _negCluster.mgh --annot lh.aparc.annot > lh parc --slabel fsaverage lh --seg --sum F_lhstats_negCluster.txt > > The problem is that this is the output of that file > (F_lhstats_negCluster.txt): > > # Title Segmentation Statistics > > # > > # generating_program mri_segstats > > # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ > > # cmdline mri_segstats --seg F_lhstats_negCluster.mgh --annot > lh.aparc.annot lh parc --slabel fsaverage lh --seg --sum > F_lhstats_negCluster.txt > > # sysname Linux > > # hostname loginnode2 > > # machine x86_64 > > # user mwagshul > > # anatomy_type volume > > # > > # SUBJECTS_DIR /home/mrrc-all/MRE_LAB/Holtzer/QdecAnalysis > > # subjectname fsaverage > > # SegVolFile F_lhstats_negCluster.mgh > > # SegVolFileTimeStamp 2019/07/18 11:21:52 > > # Annot fsaverage lh parc > > # Label fsaverage lh --seg > > # ExcludeSegId > > # Only reporting non-empty segmentations > > # VoxelVolume_mm3 1 > > # TableCol 1 ColHeader Index > > # TableCol 1 FieldName Index > > # TableCol 1 Units NA > > # TableCol 2 ColHeader SegId > > # TableCol 2 FieldName Segmentation Id > > # TableCol 2 Units NA > > # TableCol 3 ColHeader NVoxels > > # TableCol 3 FieldName Number of Voxels > > # TableCol 3 Units unitless > > # TableCol 4 ColHeader Volume_mm3 > > # TableCol 4 FieldName Volume > > # TableCol 4 Units mm^3 > > # TableCol 5 ColHeader StructName > > # TableCol 5 FieldName Structure Name > > # TableCol 5 Units NA > > # NRows 8 > > # NTableCols 5 > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName > > 1 0 161454 161454.0 Seg0000 > > *2 6 524 524.0 Seg0006* > > * 3 7 897 897.0 Seg0007* > > * 4 8 413 413.0 Seg0008* > > * 5 9 311 311.0 Seg0009* > > * 6 10 165 165.0 Seg0010* > > * 7 11 61 61.0 Seg0011* > > * 8 12 17 17.0 Seg0012* > > This clearly is reporting clusters larger than the 216 voxels reported > by mri_surfcluster. Hope someone can help us figure out the > discrepancy here, thanks! > > (As an aside, what are we doing wrong with the mri_segstats command > which is not printing out the actual anatomical locations for each > cluster?). > > Mark > > ____________________ > Mark Wagshul, PhD > Associate Professor > Gruss Magnetic Resonance Research Center > Albert Einstein College of Medicine > Bronx, NY 10461 > > Ph: 718-430-4011 > > FAX: 718-430-3399 > > Email: mark.wags...@einstein.yu.edu <mailto:mark.wags...@einstein.yu.edu> > > einstein-logo-rgb > > This email message and any accompanying attachments may contain > privileged information intended only for the named recipient(s). If > you are not the intended recipient(s), you are hereby notified that > the dissemination, distribution, and or copying of this message is > strictly prohibited. If you receive this message in error, or are not > the named recipient(s), please notify the sender at the email address > above, delete this email from your computer, and destroy any copies in > any form immediately. > > > _______________________________________________ > 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
