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