Dear Doug,
I tried using --o instead of --ocp.
Neither the sig.sum nor the sig.mgh file change.
So i dont see the postcentral cluster neither after running it with --o in sig.mgh.
But the cluster is present in the sig.sum file. i am not sure why
it could be like that.
Best Georgiana
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
-- 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