Try using --o instead of --ocp
On 08/25/2016 05:50 AM, Oana Georgiana Rus wrote: > > Dear Doug, > > thanks a lot for responding. Here my command lines and attached the image. > > *So command line to perform the GLM analysis and get the sig.mgh file > was:* > > mri_glmfit --y > /data_august/Geo/freesurfer_OCD/freesurf_steps/2_mris_preproc/education_out/rh.all_gender_age.volume.10.mgh > > \ > --fsgd diagnosis_gender_scanner_age.fsgd dods\ > --surf average_subjects rh \ > --C > /data_august/Geo/freesurfer_OCD/subjects_converted/difference_OCD_nonOCD_regressing_gender_scanner_age.mat > > \ > --C > /data_august/Geo/freesurfer_OCD/subjects_converted/difference_Muc_Jen_regressing_group_gender_age.mat > > \ > --glmdir > /data_august/Geo/freesurfer_OCD/freesurf_steps/3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir > > > > *Then to see the sig.mgh FDR corrected(0.05) and with corresponding > clusters in a text file sig.sum the command line was:* > > mri_surfcluster --src > 3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/sig.mgh > > \ > --subject average_subjects \ > --annot aparc \ > --fdr .05 \ > --hemi rh \ > --sum > 3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/FDR_corrected/sig.cluster.sum > > \ > --ocp > 3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/FDR_corrected/sig.cluster.mgh > > > > *The result output file sig.cluster.sum file looks like: * > > # Cluster Growing Summary (mri_surfcluster) > # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ > # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ > # CreationTime 2016/08/10-12:44:41-GMT > # cmdline mri_surfcluster --src > 3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/sig.mgh > > --subject average_subjects --annot aparc --fdr .05 --hemi rh --sum > 3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/FDR_corrected/sig.cluster.sum > > --ocp > 3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/FDR_corrected/sig.cluster.mgh > > > # cwd /data_august/Geo/freesurfer_OCD/freesurf_steps > # sysname Linux > # hostname dnepr.mri.tu-muenchen.de > # machine x86_64 > # FixVertexAreaFlag 1 > # FixSurfClusterArea 1 > # > # Input > 3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/sig.mgh > # Frame Number 0 > # srcsubj average_subjects > # hemi rh > # surface white > # annot aparc > # SUBJECTS_DIR /data_august/Geo/freesurfer_OCD/subjects_converted > # FDR 0.050000 > # SearchSpace_mm2 68665.3 > # SearchSpace_vtx 163842 > # Bonferroni 0 > # Minimum Threshold 2.90905 > # Maximum Threshold infinity > # Threshold Sign abs > # AdjustThreshWhenOneTail 1 > # Area Threshold 0 mm^2 > # Overall max 2.17264 at vertex 97170 > # Overall min -5.57963 at vertex 38757 > # NClusters 23 > # Total Cortical Surface Area 68665.3 (mm^2) > # FixMNI = 1 > # > # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot > 1 -5.580 38757 312.19 20.1 -49.7 9.0 738 precuneus > 2 -5.264 112198 798.03 28.5 -80.4 18.9 1067 > lateraloccipital > *3 -4.536 37472 126.77 45.4 -7.8 14.7 286 postcentral* > 4 -4.293 2509 149.21 53.8 -44.9 6.3 296 bankssts > 5 -4.238 130081 120.67 9.5 -81.0 37.6 171 > superiorparietal > 6 -4.176 70319 89.19 43.6 -45.1 -9.9 127 fusiform > 7 -4.142 99571 56.31 55.7 -13.9 18.5 135 > postcentral > 8 -3.903 114823 128.09 49.5 -28.9 -19.9 189 > inferiortemporal > 9 -3.601 2614 30.73 10.5 18.1 57.1 56 > superiorfrontal > 10 -3.540 17914 118.52 32.3 13.2 50.3 193 > caudalmiddlefrontal > 11 -3.477 73193 101.62 44.7 38.5 -5.6 124 > parstriangularis > 12 -3.422 162554 56.81 62.7 -36.1 -1.7 100 > middletemporal > 13 -3.420 49413 32.19 44.1 -0.3 -17.6 80 > superiortemporal > 14 -3.416 19541 59.40 12.9 -50.9 60.8 129 > superiorparietal > 15 -3.351 99261 28.03 38.3 40.6 4.6 36 > rostralmiddlefrontal > 16 -3.291 44544 46.46 4.3 -57.2 22.4 85 precuneus > 17 -3.275 28430 29.87 39.4 -14.7 -22.4 47 fusiform > 18 -3.266 148698 64.62 17.6 -59.8 -1.5 76 lingual > 19 -3.070 103846 21.14 48.0 31.9 -7.1 28 > parstriangularis > 20 -3.052 19099 13.00 17.8 34.1 46.5 18 > superiorfrontal > 21 -3.025 139250 23.07 34.9 -84.6 5.2 30 > lateraloccipital > 22 -3.021 71749 8.66 21.6 -46.1 -1.4 19 lingual > 23 -2.959 33038 5.73 42.7 -25.1 60.6 13 > postcentral > > *In the sig.mgh result image which is FDR corrected and attached to > the email I miss the red marked cluster (the third one).** > **See result image attached.* > > i can send you also the other views. > > Thanks a lot in advance. > > Best Georgiana > Am 23.08.2016 um 18:26 schrieb Douglas N Greve: >> Can you send the command line, the sum file, and a pic of the surface? >> >> >> On 08/23/2016 04:39 AM, Oana Georgiana Rus wrote: >>> Dear Freesurfer experts, >>> >>> I have run an analysis on GM Volume in Freesurfer. >>> >>> The interested contrast was patients vs. controls. (/command mri_glimfit/) >>> >>> I then ran /mri_surfcluster/ command to get a text file with the >>> significant clusters FDRcorrected and their peak coordinatesn- >>> resulting in a *sig.mgh image* and a *sig.sum file*. >>> >>> *After looking at the sig.mgh image with tksurfer and searching for >>> the significant clusters in the sig.sum files, I realized that one >>> cluster which is pretty big is missing in the sig.mgh image but is >>> present in the sig.sum file.* >>> >>> *Do you know why this could happen?Why is the image incomplete?* >>> >>> *Anybody encounterd something similar?* >>> >>> Because in the next step I want to extract the values of the >>> significant clusters and correlate them with clinical scores, it would >>> be good if thenumber of clusters in the result image and the result >>> file coincide. >>> >>> Thanks in advance for your help. >>> >>> Best, >>> >>> Georgiana >>> >>> >>> >>> >>> -- >>> Oana Georgiana Rus >>> PhD Student >>> Neuroimaging Center TUM-NIC >>> Klinikum rechts der Isar >>> Technische Universität München >>> Einsteinstr.1 >>> 81675 München >>> Raum 5.8 >>> >>> Tel. 089 4140 7971 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Oana Georgiana Rus > PhD Student > Neuroimaging Center TUM-NIC > Klinikum rechts der Isar > Technische Universität München > Einsteinstr.1 > 81675 München > Raum 5.8 > > Tel. 089 4140 7971 > > > _______________________________________________ > 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.
