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Dear Freesurfer support,
we met some probelm when we investigate difference between two groups. We have two sets of data, one is the TLE group, the other is the extraTLE. We also has the variables: age,gender and neuropsychological test scores. We want to analyze the relationship between cortical thickness and neuropsychological test, controlling for age, gender and group. The contrast in the full DODS model in the mri_glmfit is 0 0 0 0 0.5 0.5 0 0, with the fsgd file being: GroupDescriptorFile 1 Title MyTitle MeasurementName thickness Class Class1_TLE Class Class3_extra_TLE Variables Age factor4 gender Input PT1_01 Class1_TLE 23 12 1 Input PT1_03 Class1_TLE 38 10.26 0 Input PT1_04 Class1_TLE 26 13 0 Input PT1_06 Class1_TLE 45 13 1 Input PT1_11 Class1_TLE 20 15 1 Input PT1_12 Class1_TLE 23 10.26 0 Input PT1_14 Class1_TLE 39 9 1 Input PT1_27 Class1_TLE 51 14 1 Input PT1_32 Class1_TLE 33 11 0 Input PT1_33 Class1_TLE 27 8 1 Input PT1_34 Class1_TLE 19 8 0 Preproc was done with: mris_preproc --fsgd patients_age_gender_Arithmetic.fsgd \ --cache-in thickness.fwhm15.fsaverage \ --target fsaverage \ --hemi rh \ --out rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh
GLM was done with: mri_glmfit --y rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh \ --fsgd patients_age_gender_Arithmetic.fsgd dods \ --C difference_Arithmetic_all.mtx \ --surf fsaverage rh \ --glmdir rh_thickness_Arithmetic My questions are： (1)Are the command lines, fsgd file and the contrast matrix correct? (2)We have used qdec (DODS) to visualize the results, but I can't open the sig.mgh file. I dont know why? The terminal shows that : Reading /usr/local/freesurfer/tktools/tkUtils.tcl
Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl ERROR: MRISread: file '/usr/local/freesurfer/subjects/Neuropsychology/rh_thickness_Arithmetic/difference_Arithmetic_all/F.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!
Invalid argument
I dont know how to solve it. I very appreciate your help. Kind regards, Kan
Don't use gender as a continuous variable. You need four classes (TLE-Male, TLE-Female, etc) and change the contrast to reflect it, otherwise I think it looks ok. Load the sig.mgh file into freeview (or the tksurferfv freeview wrapper)
On 2/19/2020 10:31 PM, 邓刊 wrote:
External Email - Use Caution
Dear Freesurfer support,
we met some probelm when we investigate difference between two groups. We have two sets of data, one is the TLE group, the other is the extraTLE. We also has the variables: age,gender and neuropsychological test scores. We want to analyze the relationship between cortical thickness and neuropsychological test, controlling for age, gender and group. The contrast in the full DODS model in the mri_glmfit is 0 0 0 0 0.5 0.5 0 0, with the fsgd file being: GroupDescriptorFile 1 Title MyTitle MeasurementName thickness Class Class1_TLE Class Class3_extra_TLE Variables Age factor4 gender Input PT1_01 Class1_TLE 23 12 1 Input PT1_03 Class1_TLE 38 10.26 0 Input PT1_04 Class1_TLE 26 13 0 Input PT1_06 Class1_TLE 45 13 1 Input PT1_11 Class1_TLE 20 15 1 Input PT1_12 Class1_TLE 23 10.26 0 Input PT1_14 Class1_TLE 39 9 1 Input PT1_27 Class1_TLE 51 14 1 Input PT1_32 Class1_TLE 33 11 0 Input PT1_33 Class1_TLE 27 8 1 Input PT1_34 Class1_TLE 19 8 0 Preproc was done with: mris_preproc --fsgd patients_age_gender_Arithmetic.fsgd \ --cache-in thickness.fwhm15.fsaverage \ --target fsaverage \ --hemi rh \ --out rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh GLM was done with: mri_glmfit --y rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh \ --fsgd patients_age_gender_Arithmetic.fsgd dods \ --C difference_Arithmetic_all.mtx \ --surf fsaverage rh \ --glmdir rh_thickness_Arithmetic My questions are： (1)Are the command lines, fsgd file and the contrast matrix correct? (2)We have used qdec (DODS) to visualize the results, but I can't open the sig.mgh file. I dont know why? The terminal shows that : Reading /usr/local/freesurfer/tktools/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl ERROR: MRISread: file '/usr/local/freesurfer/subjects/Neuropsychology/rh_thickness_Arithmetic/difference_Arithmetic_all/F.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface! Invalid argument I dont know how to solve it.I very appreciate your help. Kind regards, Kan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi,Douglas, Thanks for your reply! I have changed the classes and the contrast as your suggestion. But I still met some problem when viewed the results. I still met the problem when I loaded the sig.mgh file into freeview or qdec. I still don't know how to see the result. Thank you in advance!
At 2020-02-21 06:00:57, "Douglas N. Greve" dgreve@mgh.harvard.edu wrote:
Don't use gender as a continuous variable. You need four classes (TLE-Male, TLE-Female, etc) and change the contrast to reflect it, otherwise I think it looks ok. Load the sig.mgh file into freeview (or the tksurferfv freeview wrapper)
On 2/19/2020 10:31 PM, 邓刊 wrote:
External Email - Use Caution
Dear Freesurfer support,
we met some probelm when we investigate difference between two groups. We have two sets of data, one is the TLE group, the other is the extraTLE. We also has the variables: age,gender and neuropsychological test scores. We want to analyze the relationship between cortical thickness and neuropsychological test, controlling for age, gender and group. The contrast in the full DODS model in the mri_glmfit is 0 0 0 0 0.5 0.5 0 0, with the fsgd file being: GroupDescriptorFile 1 Title MyTitle MeasurementName thickness Class Class1_TLE Class Class3_extra_TLE Variables Age factor4 gender Input PT1_01 Class1_TLE 23 12 1 Input PT1_03 Class1_TLE 38 10.26 0 Input PT1_04 Class1_TLE 26 13 0 Input PT1_06 Class1_TLE 45 13 1 Input PT1_11 Class1_TLE 20 15 1 Input PT1_12 Class1_TLE 23 10.26 0 Input PT1_14 Class1_TLE 39 9 1 Input PT1_27 Class1_TLE 51 14 1 Input PT1_32 Class1_TLE 33 11 0 Input PT1_33 Class1_TLE 27 8 1 Input PT1_34 Class1_TLE 19 8 0 Preproc was done with: mris_preproc --fsgd patients_age_gender_Arithmetic.fsgd \ --cache-in thickness.fwhm15.fsaverage \ --target fsaverage \ --hemi rh \ --out rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh
GLM was done with: mri_glmfit --y rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh \ --fsgd patients_age_gender_Arithmetic.fsgd dods \ --C difference_Arithmetic_all.mtx \ --surf fsaverage rh \ --glmdir rh_thickness_Arithmetic My questions are： (1)Are the command lines, fsgd file and the contrast matrix correct? (2)We have used qdec (DODS) to visualize the results, but I can't open the sig.mgh file. I dont know why? The terminal shows that : Reading /usr/local/freesurfer/tktools/tkUtils.tcl
Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl ERROR: MRISread: file '/usr/local/freesurfer/subjects/Neuropsychology/rh_thickness_Arithmetic/difference_Arithmetic_all/F.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!
Invalid argument
I dont know how to solve it. I very appreciate your help. Kind regards, Kan
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi,Douglas, Thanks for your reply! I have changed the classes and the contrast as your suggestion. But I still met some problem when viewed the results. I still met the problem when I loaded the sig.mgh file into freeview or qdec. I don't know how to see the result. Thank you in advance!
At 2020-02-21 06:00:57, "Douglas N. Greve" dgreve@mgh.harvard.edu wrote:
Don't use gender as a continuous variable. You need four classes (TLE-Male, TLE-Female, etc) and change the contrast to reflect it, otherwise I think it looks ok. Load the sig.mgh file into freeview (or the tksurferfv freeview wrapper)
On 2/19/2020 10:31 PM, 邓刊 wrote:
External Email - Use Caution
Dear Freesurfer support,
we met some probelm when we investigate difference between two groups. We have two sets of data, one is the TLE group, the other is the extraTLE. We also has the variables: age,gender and neuropsychological test scores. We want to analyze the relationship between cortical thickness and neuropsychological test, controlling for age, gender and group. The contrast in the full DODS model in the mri_glmfit is 0 0 0 0 0.5 0.5 0 0, with the fsgd file being: GroupDescriptorFile 1 Title MyTitle MeasurementName thickness Class Class1_TLE Class Class3_extra_TLE Variables Age factor4 gender Input PT1_01 Class1_TLE 23 12 1 Input PT1_03 Class1_TLE 38 10.26 0 Input PT1_04 Class1_TLE 26 13 0 Input PT1_06 Class1_TLE 45 13 1 Input PT1_11 Class1_TLE 20 15 1 Input PT1_12 Class1_TLE 23 10.26 0 Input PT1_14 Class1_TLE 39 9 1 Input PT1_27 Class1_TLE 51 14 1 Input PT1_32 Class1_TLE 33 11 0 Input PT1_33 Class1_TLE 27 8 1 Input PT1_34 Class1_TLE 19 8 0 Preproc was done with: mris_preproc --fsgd patients_age_gender_Arithmetic.fsgd \ --cache-in thickness.fwhm15.fsaverage \ --target fsaverage \ --hemi rh \ --out rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh
GLM was done with: mri_glmfit --y rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh \ --fsgd patients_age_gender_Arithmetic.fsgd dods \ --C difference_Arithmetic_all.mtx \ --surf fsaverage rh \ --glmdir rh_thickness_Arithmetic My questions are： (1)Are the command lines, fsgd file and the contrast matrix correct? (2)We have used qdec (DODS) to visualize the results, but I can't open the sig.mgh file. I dont know why? The terminal shows that : Reading /usr/local/freesurfer/tktools/tkUtils.tcl
Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl ERROR: MRISread: file '/usr/local/freesurfer/subjects/Neuropsychology/rh_thickness_Arithmetic/difference_Arithmetic_all/F.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!
Invalid argument
I dont know how to solve it. I very appreciate your help. Kind regards, Kan
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi,Douglas, Thanks for your reply! I have changed the classes and the contrast as your suggestion. But I still met some problem when viewed the results. I still met the problem when I loaded the sig.mgh file into freeview or qdec. I don't know how to see the result. Then I used the mri-glmfit-sim to run the cluster-based correction like this:mri_glmfit-sim --glmdir lh_sulc_digitalspan_patient --cache 2 abs --cwp 0.05.I open the file cache.th20.abs.sig.cluster.summary, with the following content: # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $ # $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ # CreationTime 2020/02/21-15:55:48-GMT # cmdline mri_surfcluster.bin --in lh_sulc_digitalspan_patient/difference_group/sig.mgh --mask lh_sulc_digitalspan_patient/mask.mgh --cwsig lh_sulc_digitalspan_patient/difference_group/cache.th20.abs.sig.cluster.mgh --sum lh_sulc_digitalspan_patient/difference_group/cache.th20.abs.sig.cluster.summary --ocn lh_sulc_digitalspan_patient/difference_group/cache.th20.abs.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh_sulc_digitalspan_patient/difference_group/cache.th20.abs.sig.masked.mgh --no-fixmni --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm16/abs/th20/mc-z.csd --csdpdf lh_sulc_digitalspan_patient/difference_group/cache.th20.abs.pdf.dat --vwsig lh_sulc_digitalspan_patient/difference_group/cache.th20.abs.sig.voxel.mgh --vwsigmax lh_sulc_digitalspan_patient/difference_group/cache.th20.abs.sig.voxel.max.dat --oannot lh_sulc_digitalspan_patient/difference_group/cache.th20.abs.sig.ocn.annot --surf white # cwd /usr/local/freesurfer/subjects/Neuropsychology # sysname Linux # hostname szu-All-Series-Invalid-entry-length-16-Fixed-up-to-11 # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input lh_sulc_digitalspan_patient/difference_group/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # group_avg_surface_area 82220 # group_avg_vtxarea_loaded 1 # annot aparc # SUBJECTS_DIR /usr/local/freesurfer/subjects # SearchSpace_mm2 74835.9 # SearchSpace_vtx 145792 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 3.02497 at vertex 6409 # Overall min -2.10431 at vertex 112918 # NClusters 0 # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot Does that mean there is no significant cluster? Is the reason that I can't open the sig.mgh? Eagerly waiting for your reply. Thank you in advance!
Don't use gender as a continuous variable. You need four classes (TLE-Male, TLE-Female, etc) and change the contrast to reflect it, otherwise I think it looks ok. Load the sig.mgh file into freeview (or the tksurferfv freeview wrapper)
On 2/19/2020 10:31 PM, 邓刊 wrote:
External Email - Use Caution
Dear Freesurfer support,
we met some probelm when we investigate difference between two groups. We have two sets of data, one is the TLE group, the other is the extraTLE. We also has the variables: age,gender and neuropsychological test scores. We want to analyze the relationship between cortical thickness and neuropsychological test, controlling for age, gender and group. The contrast in the full DODS model in the mri_glmfit is 0 0 0 0 0.5 0.5 0 0, with the fsgd file being: GroupDescriptorFile 1 Title MyTitle MeasurementName thickness Class Class1_TLE Class Class3_extra_TLE Variables Age factor4 gender Input PT1_01 Class1_TLE 23 12 1 Input PT1_03 Class1_TLE 38 10.26 0 Input PT1_04 Class1_TLE 26 13 0 Input PT1_06 Class1_TLE 45 13 1 Input PT1_11 Class1_TLE 20 15 1 Input PT1_12 Class1_TLE 23 10.26 0 Input PT1_14 Class1_TLE 39 9 1 Input PT1_27 Class1_TLE 51 14 1 Input PT1_32 Class1_TLE 33 11 0 Input PT1_33 Class1_TLE 27 8 1 Input PT1_34 Class1_TLE 19 8 0 Preproc was done with: mris_preproc --fsgd patients_age_gender_Arithmetic.fsgd \ --cache-in thickness.fwhm15.fsaverage \ --target fsaverage \ --hemi rh \ --out rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh
GLM was done with: mri_glmfit --y rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh \ --fsgd patients_age_gender_Arithmetic.fsgd dods \ --C difference_Arithmetic_all.mtx \ --surf fsaverage rh \ --glmdir rh_thickness_Arithmetic My questions are： (1)Are the command lines, fsgd file and the contrast matrix correct? (2)We have used qdec (DODS) to visualize the results, but I can't open the sig.mgh file. I dont know why? The terminal shows that : Reading /usr/local/freesurfer/tktools/tkUtils.tcl
Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl ERROR: MRISread: file '/usr/local/freesurfer/subjects/Neuropsychology/rh_thickness_Arithmetic/difference_Arithmetic_all/F.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!
Invalid argument
I dont know how to solve it. I very appreciate your help. Kind regards, Kan
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
邓刊