PRSice and R lm() show different association analysis output (coefficient, SE and P)

[Salahuddin Mohammad]

Hey,
I am struggling to understand Why am I getting different association analysis output (coefficient, SE and P) between PRSice and lm() function in R.
Not only the values, even the direction of association is different.
I am trying to do association analysis between PRS of my trait and MRI data in UKB. Feeding PRSice the standardized phenotype data.  
Fraction of output from PRSice:
Pheno Coefficient Standard.Error P Threshold
Zcortical_vol2 0.447657 0.573909 0.435388 0.001
Zcortical_vol2 1.17785 1.46062 0.420018 0.01
Zcortical_vol2 1.34621 3.77899 0.721667 0.1
Zcortical_vol2 5.35868 5.51758 0.331455 0.25
Zcortical_vol2 8.51688 7.31505 0.244313 0.5
Zcortical_vol2 8.13715 8.40917 0.333226 0.75
Zcortical_vol2 7.3802 9.07108 0.415883 1
ZCSF_vol2 0.148759 0.603998 0.805459 0.001
ZCSF_vol2 0.496379 1.5372 0.746765 0.01
ZCSF_vol2 1.34283 3.97707 0.735635 0.1
ZCSF_vol2 3.49077 5.80685 0.547747 0.25
ZCSF_vol2 -0.0165925 7.69866 0.99828 0.5
ZCSF_vol2 0.706873 8.8501 0.93634 0.75
ZCSF_vol2 -0.961857 9.54667 0.919747 1
ZGM_vol2 0.348648 0.569733 0.540576 0.001
ZGM_vol2 0.639184 1.45 0.659349 0.01
ZGM_vol2 -0.176105 3.75148 0.962559 0.1
ZGM_vol2 1.72553 5.47748 0.752747 0.25
ZGM_vol2 4.15182 7.26191 0.567512 0.5
ZGM_vol2 4.44471 8.34804 0.594434 0.75
ZGM_vol2 3.88854 9.00511 0.665879 1

......
Fraction of out put from R using lm() function:
β SE P value Threshold
cortical_vol2 -121 211.49 0.5672 0.001
cortical_vol2 75.2 214.63 0.7261 0.01
cortical_vol2 67.02 225.98 0.7668 0.1
cortical_vol2 5.16 228.77 0.982 0.25
cortical_vol2 -85.61 229.97 0.7097 0.5
cortical_vol2 -85.86 231.22 0.7104 0.75
cortical_vol2 -82.1 231.09 0.7224 1
CSF_vol2 249.66 86.6 0.0039 0.001
CSF_vol2 190 87.89 0.0306 0.01
CSF_vol2 155.93 92.54 0.092 0.1
CSF_vol2 142.29 93.68 0.1288 0.25
CSF_vol2 131.52 94.17 0.1626 0.5
CSF_vol2 139.53 94.68 0.1406 0.75
CSF_vol2 139.83 94.63 0.1395 1
GM_vol2 -196.13 252.48 0.4373 0.001
GM_vol2 2.54 256.23 0.9921 0.01
GM_vol2 -7.48 269.78 0.9779 0.1
GM_vol2 -84.56 273.11 0.7568 0.25
GM_vol2 -187.53 274.53 0.4946 0.5
GM_vol2 -179.24 276.03 0.5161 0.75
GM_vol2 -174.84 275.88 0.5263 1
.....
My script for association analysis in PRSice where I used previouly clumped PRS:
PRSice 2.3.5 (2021-09-20)
https://github.com/choishingwan/PRSice
(C) 2016-2020 Shing Wan (Sam) Choi and Paul F. O'Reilly
GNU General Public License v3
If you use PRSice in any published work, please cite:
Choi SW, O'Reilly PF.
PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data.
GigaScience 8, no. 7 (July 1, 2019)
2024-02-06 09:38:16
D:\ukb_genetic_data\PRSice_win64.exe \
    --a1 A1 \
    --a2 A2 \
    --allow-inter  \
    --bar-levels 0.001,0.01,0.1,0.25,0.5,0.75,1 \
    --base iPSYCH-PGC_ASD_Nov2017.gz \
    --base-info INFO:0.9 \
    --beta  \
    --binary-target 46F \
    --bp BP \
    --chr CHR \
    --cov mig_asd_cov \
    --cov-col scan_x_pos,scan_y_pos,scan_z_pos,Zage,Zsex,Zbatch,@Zpc[1-20] \
    --cov-factor Zsex,Zbatch \
    --extract ukb_distribution_011023.snp \
    --fastscore  \
    --geno 0.02 \
    --ignore-fid  \
    --no-clump  \
    --num-auto 22 \
    --out mri_asd_run_060224 \
    --pheno cerebelum_pheno_060224 \
    --pheno-col eid,Zcortical_vol2,ZCSF_vol2,ZGM_vol2,ZWM_vol2,ZTBV2,ZWMH_vol2,ZBrainStem_vol2,ZI_IVCerebellum_L_vol2,ZI_IVCerebellum_R_vol2,ZVCerebellum_L_vol2,ZVCerebellum_R_vol2,ZVICerebellum_L_vol2,ZVermisVICerebellum_vol2,ZVICerebellum_R_vol2,ZCrusICerebellum_L_vol2,ZVermisCrusICerebellum_vol2,ZCrusICerebellum_R_vol2,ZCrusIICerebellum_L_vol2,ZVermisCrusIICerebellum_vol2,ZCrusIICerebellum_R_vol2,ZVIIbCerebellum_L_vol2,ZVermisVIIbCerebellum_vol2,ZVIIbCerebellum_R_vol2,ZVIIIaCerebellum_L_vol2,ZVermisVIIIaCerebellum_vol2,ZVIIIaCerebellum_R_vol2,ZVIIIbCerebellum_L_vol2,ZVermisVIIIbCerebellum_vol2,ZVIIIbCerebellum_R_vol2,ZIXCerebellum_L_vol2,ZVermisIXCerebellum_vol2,ZIXCerebellum_R_vol2,ZXCerebellum_L_vol2,ZVermisXCerebellum_vol2,ZXCerebellum_R_vol2,ZI_IVCerebellum_vol2,ZVCerebellum_vol2,ZVICerebellum_vol2,ZVIIbCerebellum_vol2,ZVIIIaCerebellum_vol2,ZVIIIbCerebellum_vol2,ZIXCerebellum_vol2,ZXCerebellum_vol2,ZCrusICerebellum_vol2,ZCrusIICerebellum_vol2 \
    --print-snp  \
    --pvalue P \
    --seed 1435821109 \
    --snp SNP \
    --stat OR \
    --target ukb_imp_chr#_v3,ukb30172_imp_chr22_v3_s487324.sample \
    --thread 1 \
    --type bgen

Your input is highly appreciated.

Thanks

Sal