T values and alphasim

Submitted by Giselle on

Dear Prof Yan,

Thank you for your response.

  1. For FWHM values, it was obtained from DPABI->Statistical Analysis without PALM; the values are (FWHM, in mm) = [1.524, 1.389, 1.300]. You commented that it seems too small, can I check what can be done about this?

 

  1. The reason why I am doing TFCE+alphasim is because none of the voxels survived after TFCE+additional thresholding, but I do have voxels which survive from TFCE + alphasim. Is my understanding that TFCE+FWE just different methods of correcting as compared to TFCE+alphasim albeit at cluster level?

 

  1. When I load T2_tfce_tstat.nii as my overlay and did alphasim at p of 0.001 and alpha of 0.05, I obtained this:

Mask filename = GroupMask90Percent

Voxels in mask = 54149

Gaussian filter width (FWHM, in mm) = [1.524, 1.389, 1.300]

Individual voxel threshold probability = 0.001

Number of Monte Carlo simulations = 1000

Cl Size    Frequency           Cum Prop            p/Voxel Max Freq             Alpha

1                            52262                   0.993933             0.000977             723                       1.000000

2                            310                       0.999829             0.000012             268                       0.277000

3                            8                            0.999981             0.000001             8                            0.009000

4                            1                            1.000000             0.000000             1                            0.001000

For alpha 0.05, I have 2 clusters, cluster size of 1 and 8. When I ran the cluster report for cluster size 1 and 8, Precentral Gyrus was identified, peak intensity of 140.2

     3a) Can I check in terms of interpretation, cluster 3 (size of 8) corresponds to only precentral gyrus or does it mean that this cluster might also consist of other brain regions?

 

      3b) With the cluster report, we get the peak intensity, can I kindly check how to we obtain the T-values (I ran 2-samples t-test previously)

 

      3c) A related question is, how do I obtain a T-map which can be loaded onto MRIcron which will display T-values– right now, I only have the intensity values

 

  1. In terms of FC analysis, if I have 2 seeds, do I have to run FC analyses twice within DPARSF with the 2 separate seeds or can I define both seeds within 1 FC analysis run?

Thank you.

Giselle

YAN Chao-Gan

Wed, 09/02/2020 - 02:24

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1. What kind of maps are you using? I have never seen such small FWHM in real data.

2. If there is no results after TFCE correction, then there is no results. "TFCE + alphasim" is not a valid method.

3. Not valid methods.

4. You can run once by adding two ROIs.

Dear Prof Yan,

Thank you.

I appreciate that it does not make sense to perform tfce+alphasim

If I were to just perform alphasim with no tfce, can I check the following:

1) Which .nii file from the 2 sample t-test should I load within DPABI viewer in order to perform alphasim. I chose T2_vox_tstat.nii.

 

2) This is the alpasim output I obtained from p 0.001

Mask filename = GroupMask90Percent

Voxels in mask = 54149

Gaussian filter width (FWHM, in mm) = [4.573, 4.167, 3.901]

Individual voxel threshold probability = 0.001

Number of Monte Carlo simulations = 1000

Cl Size    Frequency           Cum Prop            p/Voxel Max Freq             Alpha

1                            44013                   0.919082             0.000966             22                          1.000000

2                            3423                     0.990561             0.000153             607                       0.978000

3                            381                       0.998517             0.000027             303                       0.371000

4                            55                          0.999666             0.000006             52                          0.068000

5                            15                          0.999979             0.000001             15                          0.016000

6                            1                            1.000000             0.000000             1                            0.001000

Am I right to interpret this such that at alpha of 0.05, number of voxels is 15?

 

3) So if step 2 is correct and I ran cluster report with number of voxels as 15, I got this cluster report (only 1 cluster was found):

Number of voxels: 54136

Peak MNI coordinate: -54  18  27

Peak MNI coordinate region:  // Left Cerebrum // Frontal Lobe // Inferior Frontal Gyrus // Gray Matter // brodmann area 9 // Frontal_Inf_Tri_L (aal)

Peak intensity: -4.5132

# voxels            structure

54136 --TOTAL # VOXELS--

28634 White Matter

22869 Right Cerebrum

22720 Left Cerebrum

15854 Frontal Lobe

14157 Gray Matter

 7323   Parietal Lobe

 6989   Temporal Lobe

 6958   Sub-Gyral

 6553   Sub-lobar

 4607   Occipital Lobe

 4216   Limbic Lobe

 3410   Cerebellum Posterior Lobe

 3275   Middle Frontal Gyrus

 3016   Extra-Nuclear

 2692   Left Cerebellum

 2644   Right Cerebellum

 2359   Superior Frontal Gyrus

 2219   Precuneus

 2139   Superior Temporal Gyrus

 2064   Middle Temporal Gyrus

 2042   Medial Frontal Gyrus

 2018   Precentral Gyrus

 1946   Inferior Frontal Gyrus

 1904   Cingulate Gyrus

 1903   Cerebellum Anterior Lobe

 1765   Postcentral Gyrus

 1643   Inferior Parietal Lobule

 1580   brodmann area 6

 1419   Cuneus

 1400   Culmen

 1274   Frontal_Mid_R (aal)

 1242   Declive

 1205   Frontal_Mid_L (aal)

 1157   Insula

 1085   Temporal_Mid_L (aal)

 1020   Cerebellar Tonsil

  999     Middle Occipital Gyrus

  995     Frontal_Sup_R (aal)

  988     Lingual Gyrus

  962     Postcentral_L (aal)

  952     brodmann area 7

  885     Parahippocampa Gyrus

  862     Postcentral_R (aal)

  862     Temporal_Mid_R (aal)

  856     Inter-Hemispheric

  845     Precentral_L (aal)

  837     Precuneus_L (aal)

  835     Precuneus_R (aal)

  833     Occipital_Mid_L (aal)

  830     Frontal_Sup_L (aal)

  784     brodmann area 40

  773     Anterior Cingulate

  765     Precentral_R (aal)

  739     Corpus Callosum

  718     Left Brainstem

  695     Cerebro-Spinal Fluid

  679     Parietal_Inf_L (aal)

  674     Fusiform Gyrus

  671     Temporal_Sup_R (aal)

  666     Right Brainstem

  654     Lateral Ventricle

  646     Frontal_Sup_Medial_L (aal)

  639     brodmann area 19

  638     Supp_Motor_Area_R (aal)

  637     Midbrain

  636     brodmann area 9

  636     Pons

  628     Temporal_Sup_L (aal)

  621     Lentiform Nucleus

  612     Frontal_Inf_Tri_L (aal)

  606     brodmann area 18

  595     Calcarine_L (aal)

  595     Thalamus

  593     Cingulum_Mid_R (aal)

  583     Calcarine_R (aal)

  583     Lingual_R (aal)

  582     Posterior Cingulate

  581     Supp_Motor_Area_L (aal)

  558     brodmann area 10

  554     Frontal_Sup_Medial_R (aal)

  552     Cingulum_Mid_L (aal)

  530     Cerebelum_Crus1_L (aal)

  513     Fusiform_R (aal)

  509     Lingual_L (aal)

  502     Fusiform_L (aal)

  492     Insula_R (aal)

  486     Cerebelum_6_L (aal)

  483     Cerebelum_6_R (aal)

  482     Insula_L (aal)

  475     Putamen

  473     brodmann area 13

  467     SupraMarginal_R (aal)

  461     Paracentral Lobule

  459     Frontal_Inf_Tri_R (aal)

  458     Occipital_Mid_R (aal)

  456     Cerebelum_Crus1_R (aal)

  444     brodmann area 31

  430     Parietal_Sup_L (aal)

  423     brodmann area 8

  420     Superior Parietal Lobule

  416     brodmann area 32

  412     Supramarginal Gyrus

  396     Angular_R (aal)

  394     Temporal_Inf_R (aal)

  391     Frontal_Inf_Orb_L (aal)

  386     Cingulum_Ant_L (aal)

  374     brodmann area 21

  368     Cingulum_Ant_R (aal)

  365     Cerebelum_8_R (aal)

  362     Cerebelum_8_L (aal)

  357     Caudate

  355     Cuneus_L (aal)

  351     Cuneus_R (aal)

  350     brodmann area 4

  345     Occipital_Sup_R (aal)

  343     Frontal_Inf_Oper_R (aal)

  339     Rolandic_Oper_R (aal)

  338     Cerebelum_4_5_L (aal)

  338     SupraMarginal_L (aal)

  335     Occipital_Sup_L (aal)

  334     brodmann area 3

  331     Parietal_Sup_R (aal)

  329     Temporal_Inf_L (aal)

  327     Paracentral_Lobule_L (aal)

  322     brodmann area 24

  321     Parietal_Inf_R (aal)

  312     Pyramis

  311     Frontal_Inf_Orb_R (aal)

  303     Angular_L (aal)

  301     brodmann area 22

  295     Thalamus_L (aal)

  294     Cerebelum_Crus2_L (aal)

  290     Thalamus_R (aal)

  285     Uvula

  275     Inferior Semi-Lunar Lobule

  275     Putamen_R (aal)

  273     brodmann area 39

  270     Hippocampus_R (aal)

  268     Putamen_L (aal)

  263     Caudate_L (aal)

  262     Hippocampus_L (aal)

  260     Caudate_R (aal)

  259     Frontal_Inf_Oper_L (aal)

  257     Occipital_Inf_L (aal)

  252     brodmann area 47

  252     brodmann area 37

  248     Rolandic_Oper_L (aal)

  242     Tuber

  239     Temporal_Pole_Sup_L (aal)

  238     Cerebelum_Crus2_R (aal)

  231     Cerebelum_9_L (aal)

  227     Cerebelum_4_5_R (aal)

  224     Inferior Temporal Gyrus

  220     brodmann area 38

  216     Temporal_Pole_Sup_R (aal)

  208     Cerebelum_9_R (aal)

  198     Angular Gyrus

  198     Paracentral_Lobule_R (aal)

  190     ParaHippocampal_R (aal)

  188     brodmann area 2

  184     brodmann area 30

  177     Transverse Temporal Gyrus

  174     Occipital_Inf_R (aal)

  171     brodmann area 5

  171     Vermis_4_5 (aal)

  169     Caudate Body

  162     Inferior Occipital Gyrus

  156     Caudate Head

  152     ParaHippocampal_L (aal)

  151     Frontal_Med_Orb_R (aal)

  146     brodmann area 11

  138     Claustrum

  136     brodmann area 17

  134     brodmann area 41

  129     Frontal_Mid_Orb_L (aal)

  129     Cingulum_Post_L (aal)

  129     Temporal_Pole_Mid_R (aal)

  126     Pulvinar

  120     brodmann area 46

  119     Frontal_Mid_Orb_R (aal)

  118     brodmann area 20

  117     brodmann area 44

  114     Dentate

  113     Cingulum_Post_R (aal)

  111     Medulla

  110     Vermis_6 (aal)

  110     Frontal_Med_Orb_L (aal)

  107     brodmann area 23

  105     Lateral Globus Pallidus

   94      brodmann area 45

   90      Cerebelum_7b_L (aal)

   84      Medial Dorsal Nucleus

   82      Pallidum_L (aal)

   79      Temporal_Pole_Mid_L (aal)

   77      Amygdala

   77      Pallidum_R (aal)

   74      Ventral Lateral Nucleus

   73      Hippocampus

   68      Heschl_R (aal)

   67      brodmann area 42

   66      Vermis_8 (aal)

   65      Heschl_L (aal)

   64      Nodule

   62      Vermis_3 (aal)

   62      Frontal-Temporal Space

   61      Uncus

   60      Superior Occipital Gyrus

   59      Amygdala_R (aal)

   59      Amygdala_L (aal)

   57      brodmann area 36

   55      brodmann area 43

   54      Cerebellar Lingual

   50      Cerebelum_3_R (aal)

   47      Cerebelum_7b_R (aal)

   47      Frontal_Sup_Orb_L (aal)

   47      Ventral Anterior Nucleus

   47      Frontal_Sup_Orb_R (aal)

   44      Vermis_7 (aal)

   44      Vermis_9 (aal)

   43      brodmann area 29

   41      Cerebelum_3_L (aal)

   40      brodmann area 28

   39      brodmann area 34

   38      brodmann area 1

   37      Medial Globus Pallidus

   36      brodmann area 35

   32      Caudate Tail

   30      Cerebelum_10_L (aal)

   30      Subcallosal Gyrus

   26      Mammillary Body

   25      Vermis_10 (aal)

   24      Declive of Vermis

   24      Third Ventricle

   22      Olfactory_L (aal)

   22      Olfactory_R (aal)

   22      Cerebelum_10_R (aal)

   21      Fastigium

   21      Red Nucleus

   21      Substania Nigra

   19      Vermis_1_2 (aal)

   19      Ventral Posterior Lateral Nucleus

   18      Culmen of Vermis

   17      Rectus_R (aal)

   14      Rectus_L (aal)

   13      brodmann area 33

   13      Fourth Ventricle

   12      Subthalamic Nucleus

   12      Lateral Posterior Nucleus

   10      Optic Tract

   10      Lateral Dorsal Nucleus

    9        Ventral Posterior Medial Nucleus

    9        brodmann area 27

    8        Uvula of Vermis

    6        Hypothalamus

    5        brodmann area 25

    5        Medial Geniculum Body

    4        Tuber of Vermis

    4        Pyramis of Vermis

    3        Lateral Geniculum Body

    2        Midline Nucleus

I interpret this to be that there is only one peak region of brodmann area 9 and that the MNI coordinates of -54  18  27 should be entered as my seed region for the next FC analysis? I am really stuck on how to identify seed regions based on the cluster report, with alphasim table indicating number of voxels of 15, can you kindly provide information/instructions please?

 

4) If I want to view the image of voxels post alphasim and clsuter report within DPABI viewer or MRIcron, how can I find this image as only cluster report and alphasim table is obtained post alphasim. I am hoping to do this to check which brain regions should I choose as my ROIs.

 

5) With the cluster report, we get the peak intensity, can I kindly check how to we obtain the T-values (I ran 2-samples t-test previously)

 

6) A related question is, how do I obtain a T-map which can be loaded onto MRIcron which will display T-values– right now, I only have the intensity values

 

 7) If I were to do multiple regression within SPM, can I simply use each individuals’ zROIFCmap.nii for 2nd level analysis or will I have to do additional changes?

 

I know the questions are simple but I really want to understand the steps/program as I am quite stuck, thank you again. 

Giselle

1.2.3. I am not sure which stop you are wrong, but the results doesn't make sense. Please use GRF correction instead.

4. As thre results doesn't make sense, I suggest not to go further.

5. Peask intensity is t value.

6. Same as 5.

7. You can.

Thank you for your reply, I re-ran the analysis but obtained the same results for alphasim.

  1. As suggested, I did GRF and one of the cluster that survived had peak intensity of -3.67, voxels in DPABI viewer corresponding to only blue regions of the colourbar (-3, -4 in colour bar). Can I check my interpretation - if I have entered patients fMRI files first followed by controls in the 2 sample t-tests, does that means patients have lower ReHo activity as compared to controls?

 

  1. In the cluster report for GRF, there is this statement, “The voxel T threshold for voxel p threshold 0.001000 is: 3.19078”, can I check what does this refer to please?

 

  1. I will like to have more clarity on how best to identify region from cluster report, if I have this:

 

Number of voxels: 19

Peak MNI coordinate: -9 -99  15

Peak MNI coordinate region:  // Left Cerebrum // Occipital Lobe // Cuneus // Gray Matter // brodmann area 18 // Occipital_Sup_L (aal)

Peak intensity: -4.2346

# voxels           structure

   19     --TOTAL # VOXELS--

   19     Left Cerebrum

   19     Occipital Lobe

   14     Cuneus

   11     Occipital_Sup_L (aal)

   10     White Matter

    9      brodmann area 18

    9      Gray Matter

    5      Middle Occipital Gyrus

    5      Cuneus_L (aal)

    3      Occipital_Mid_L (aal)

 

3a) What will you recommend to be the best way to identify region. I tried MRIcron but noticed that at times, when I enter the MNI coordinates, the brodman region can be different from that listed in the cluster report. Peak MNI coordinate region:  // Left Cerebrum // Occipital Lobe // Cuneus // Gray Matter // brodmann area 18 // Occipital_Sup_L (aal) ------ should I be using particular aspects of this to report the region in my paper or should I be looking at the vertical list just above this question?

 

Thank you for your help.

1. Yes.

2. This is T threshold for voxel p threshold 0.001.

3. I think your regions is probably Occipital_Sup_L.

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